31 Jul
2019
31 Jul
'19
2:11 p.m.
External Email - Use Caution
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
1 Aug
1 Aug
3:14 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
Please, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude miracooloz@gmail.com Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve freesurfer@nmr.mgh.harvard.edu
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
9:43 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use Caution
Please, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
2 Aug
2 Aug
3:56 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
Hello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvr1.mtx= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvr2.mtx= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use CautionPlease, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude miracooloz@gmail.com Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve freesurfer@nmr.mgh.harvard.edu
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists:
GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
5 Aug
5 Aug
12:13 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
That mostly looks good.
I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask.
The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups.
1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr.
On 8/2/2019 3:56 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvr1.mtx= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvr2.mtx= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use Caution
Please, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
3:11 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
Hello Doug,
Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht...), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct.
Thank you. Paul.
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
That mostly looks good.
I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask.
The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups.
- will my fsgd file contain both groups?
yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr.
On 8/2/2019 3:56 PM, miracle ozzoude wrote:
External Email - Use CautionHello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions.
- will my fsgd file contain both groups?
- If the answer from question is yes, i should have 2 contrasts (pvr1.mtx
for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists:
GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16
Input YY1 g2 62 20
matrix for group1:
pvr1.mtx= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvr2.mtx= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use CautionPlease, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude miracooloz@gmail.com Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve freesurfer@nmr.mgh.harvard.edu
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists:
GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
3:52 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
Yes, that contrast is correct.
On 8/5/2019 3:11 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Doug,
Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht...), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct.
Thank you. Paul.
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: That mostly looks good.
I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask.
The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups.
1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr.
On 8/2/2019 3:56 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvr1.mtx= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvr2.mtx= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use Caution
Please, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
4:39 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right. Best, Paul. Sent from my Samsung Galaxy smartphone. -------- Original message --------From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr Yes, that contrast is correct.
On 8/5/2019 3:11 PM, miracle ozzoude wrote:
External Email - Use Caution Hello Doug,
Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct.
Thank you. Paul.
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir
mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
That mostly looks good.
I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask.
The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups.
1) will my fsgd file contain both groups? yes, see above
2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it.
3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr.
On 8/2/2019 3:56 PM, miracle ozzoude wrote:
External Email - Use Caution Hello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2
mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2
mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere
fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvr1.mtx= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvr2.mtx= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using
fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use Caution Please, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude miracooloz@gmail.com Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve freesurfer@nmr.mgh.harvard.edu
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14 Input YY1 g2 62 20 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvrgroup1= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvrgroup2= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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6:45 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr)
On 8/5/2019 4:39 PM, miracooloz wrote:
External Email - Use Caution
Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right.
Best, Paul.
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
Yes, that contrast is correct.
On 8/5/2019 3:11 PM, miracle ozzoude wrote:
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Hello Doug,
Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht...), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct.
Thank you. Paul.
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: That mostly looks good.
I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask.
The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups.
1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr.
On 8/2/2019 3:56 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvr1.mtx= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvr2.mtx= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use Caution
Please, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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8:14 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
I think i got it now. Something like this:
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr)
On 8/5/2019 4:39 PM, miracooloz wrote:
External Email - Use CautionThanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right.
Best, Paul.
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu DGREVE@mgh.harvard.edu Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
Yes, that contrast is correct.
On 8/5/2019 3:11 PM, miracle ozzoude wrote:
External Email - Use CautionHello Doug,
Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht...), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct.
Thank you. Paul.
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
That mostly looks good.
I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask.
The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups.
- will my fsgd file contain both groups?
yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr.
On 8/2/2019 3:56 PM, miracle ozzoude wrote:
External Email - Use CautionHello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions.
- will my fsgd file contain both groups?
- If the answer from question is yes, i should have 2 contrasts
(pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists:
GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16
Input YY1 g2 62 20
matrix for group1:
pvr1.mtx= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvr2.mtx= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use CautionPlease, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude miracooloz@gmail.com Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve freesurfer@nmr.mgh.harvard.edu
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists:
GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
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10:17 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
I think there is still something not right. You should just have one mri_glmfit command for each hemisphere in which the input is ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the same as the first but with a reversed sign, but it is not necessary since we always use unsigned tests and show both signs (but you can still do it).
On 8/5/2019 8:14 PM, miracle ozzoude wrote:
External Email - Use Caution
I think i got it now. Something like this:
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr)
On 8/5/2019 4:39 PM, miracooloz wrote:
External Email - Use Caution
Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right.
Best, Paul.
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
Yes, that contrast is correct.
On 8/5/2019 3:11 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Doug,
Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht...), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct.
Thank you. Paul.
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: That mostly looks good.
I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask.
The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups.
1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr.
On 8/2/2019 3:56 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvr1.mtx= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvr2.mtx= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
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Please, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude <miracooloz@gmail.commailto:miracooloz@gmail.com> Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
-------------------------------------------------------------
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
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7 Aug
7 Aug
9:26 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
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Got it. Thanks a lot doug. If i have to correct for multiple comparison in surface based pet analysis and mutlimodal analysis (pet and thickness), should i use --3spaces? Thank you.
best, Paul
On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
I think there is still something not right. You should just have one mri_glmfit command for each hemisphere in which the input is ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the same as the first but with a reversed sign, but it is not necessary since we always use unsigned tests and show both signs (but you can still do it).
On 8/5/2019 8:14 PM, miracle ozzoude wrote:
External Email - Use CautionI think i got it now. Something like this:
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr)
On 8/5/2019 4:39 PM, miracooloz wrote:
External Email - Use CautionThanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right.
Best, Paul.
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu DGREVE@mgh.harvard.edu Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
Yes, that contrast is correct.
On 8/5/2019 3:11 PM, miracle ozzoude wrote:
External Email - Use CautionHello Doug,
Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht...), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct.
Thank you. Paul.
## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 1 -1
##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
That mostly looks good.
I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask.
The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups.
- will my fsgd file contain both groups?
yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr.
On 8/2/2019 3:56 PM, miracle ozzoude wrote:
External Email - Use CautionHello Doug,
Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune
##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz
##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz
##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz
##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz
###-----repeat steps 1-8 for cortical thickness-------
###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir
###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir
My questions.
- will my fsgd file contain both groups?
- If the answer from question is yes, i should have 2 contrasts
(pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct?
Thank you very much. Paul.
The fsgd file lists:
GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16
Input YY1 g2 62 20
matrix for group1:
pvr1.mtx= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvr2.mtx= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2
On 8/1/2019 3:14 PM, miracle ozzoude wrote:
External Email - Use CautionPlease, can anyone help me with this. Thank you
Paul
---------- Forwarded message --------- From: miracle ozzoude miracooloz@gmail.com Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve freesurfer@nmr.mgh.harvard.edu
Hello Experts,
I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education).
However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions.
Thank you.
Best, Paul
The fsgd file lists:
GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2
Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14
Input YY1 g2 62 20
Input YY1 g2 62 20
matrix for group1:
pvrgroup1= 1 0 0 0 0 0 0
is there a relationship between amyloid-thickness in group1 regressing out age
and education?
matrix for group2:
pvrgroup2= 0 1 0 0 0 0 0
is there a relationship between amyloid-thickness in group2 regressing out age
and education?
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11:06 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
The 3 spaces is for left hemi, right hemi, and subcortical, so, if you are using all three then correct for all 3
On 8/7/19 9:26 AM, miracle ozzoude wrote:
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Got it. Thanks a lot doug. If i have to correct for multiple comparison in surface based pet analysis and mutlimodal analysis (pet and thickness), should i use --3spaces? Thank you.
best, Paul
On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I think there is still something not right. You should just have one mri_glmfit command for each hemisphere in which the input is ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the same as the first but with a reversed sign, but it is not necessary since we always use unsigned tests and show both signs (but you can still do it). On 8/5/2019 8:14 PM, miracle ozzoude wrote:External Email - Use Caution I think i got it now. Something like this: ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr) On 8/5/2019 4:39 PM, miracooloz wrote:External Email - Use Caution Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right. Best, Paul. Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu> Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr Yes, that contrast is correct. On 8/5/2019 3:11 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct. Thank you. Paul. ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: That mostly looks good. I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask. The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups. 1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr. On 8/2/2019 3:56 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune ##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune ##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz ##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz ##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz ##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz ##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz ##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz ###-----repeat steps 1-8 for cortical thickness------- ###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir ###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct? Thank you very much. Paul. The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvr1.mtx= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvr2.mtx= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education? On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2 On 8/1/2019 3:14 PM, miracle ozzoude wrote:External Email - Use Caution Please, can anyone help me with this. Thank you Paul ---------- Forwarded message --------- From: *miracle ozzoude* <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Hello Experts, I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education). However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions. Thank you. Best, Paul The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14 Input YY1 g2 62 20 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvrgroup1= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvrgroup2= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
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Thanks Doug. Another question, how do i find the p-values for voxel-wise map corrected for multiple comparisons at a voxel (rather than cluster) level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. Best, Paul
On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
The 3 spaces is for left hemi, right hemi, and subcortical, so, if you are using all three then correct for all 3
On 8/7/19 9:26 AM, miracle ozzoude wrote:
External Email - Use CautionGot it. Thanks a lot doug. If i have to correct for multiple comparison in surface based pet analysis and mutlimodal analysis (pet and thickness), should i use --3spaces? Thank you.
best, Paul
On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I think there is still something not right. You should just have one mri_glmfit command for each hemisphere in which the input is ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the same as the first but with a reversed sign, but it is not necessary since we always use unsigned tests and show both signs (but you can still do it). On 8/5/2019 8:14 PM, miracle ozzoude wrote:External Email - Use Caution I think i got it now. Something like this: ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr) On 8/5/2019 4:39 PM, miracooloz wrote:External Email - Use Caution Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right. Best, Paul. Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu> Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr Yes, that contrast is correct. On 8/5/2019 3:11 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct. Thank you. Paul. ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>wrote:
That mostly looks good. I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask. The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups. 1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr. On 8/2/2019 3:56 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune ##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune ##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz ##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz ##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz ##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz ##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz ##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz ###-----repeat steps 1-8 for cortical thickness------- ###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir ###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct? Thank you very much. Paul. The fsgd file lists:
GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input YY1 g2 62 20
matrix for group1: pvr1.mtx= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness ingroup1 regressing out age
and education? matrix for group2: pvr2.mtx= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness ingroup2 regressing out age
and education? On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2 On 8/1/2019 3:14 PM, miracle ozzoude wrote:> > External Email - Use Caution > > Please, can anyone help me with this. > Thank you > > Paul > > ---------- Forwarded message --------- > From: *miracle ozzoude* <miracooloz@gmail.com > mailto:miracooloz@gmail.com> > Date: Wed, Jul 31, 2019 at 2:11 PM > Subject: multimodal analysis (pet and cortical > thickness relationship) using --pvr > To: Douglas N Greve > <freesurfer@nmr.mgh.harvard.edu > mailto:freesurfer@nmr.mgh.harvard.edu> > > > Hello Experts, > > I am performing an analysis looking at the > relationship between amyloid uptake and cortical > thickness using --pvr flag in mri_glmfit. I've 2 > groups and 2 variables (age and education). I > want to run a within group analysis while > regressing out age and education (i.e. Within > group 1, is there a negative relationship between > amyloid uptake and cortical thickness regressing > out the effects of age and education). > > However, i'm not sure how my pvr contrasts will > look like. Below are my fsgd and an attempt at > creating contrasts. Please, can you let me know > if my contrasts are correct based on my questions. > > Thank you. > > Best, > Paul > > The fsgd file lists: >
> GroupDescriptorFile 1 > Title Relationship Amy-thick reg out age and
education
> Class g1 > Class g2 > Variable Age Education > Input XX1 g1 60 16 > Input XX2 g1 58 14 > Input YY1 g2 62 20 > Input YY1 g2 62 20 >
> matrix for group1: > pvrgroup1= 1 0 0 0 0 0 0 > is there a relationship between amyloid-thickness
in group1 regressing out age
> and education? > matrix for group2: > pvrgroup2= 0 1 0 0 0 0 0 > is there a relationship between amyloid-thickness
in group2 regressing out age
> and education? > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
>
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11:18 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
I'm not sure what you are looking for. The voxel-wise analysis is voxel-wise, so there is no summary file for it
On 8/12/2019 11:13 AM, miracle ozzoude wrote:
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Thanks Doug. Another question, how do i find the p-values for voxel-wise map corrected for multiple comparisons at a voxel (rather than cluster) level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. Best, Paul
On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: The 3 spaces is for left hemi, right hemi, and subcortical, so, if you are using all three then correct for all 3
On 8/7/19 9:26 AM, miracle ozzoude wrote:
External Email - Use CautionGot it. Thanks a lot doug. If i have to correct for multiple comparison in surface based pet analysis and mutlimodal analysis (pet and thickness), should i use --3spaces? Thank you.
best, Paul
On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote:
I think there is still something not right. You should just have one mri_glmfit command for each hemisphere in which the input is ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the same as the first but with a reversed sign, but it is not necessary since we always use unsigned tests and show both signs (but you can still do it). On 8/5/2019 8:14 PM, miracle ozzoude wrote:External Email - Use Caution I think i got it now. Something like this: ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote: It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr) On 8/5/2019 4:39 PM, miracooloz wrote:External Email - Use Caution Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right. Best, Paul. Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr Yes, that contrast is correct. On 8/5/2019 3:11 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct. Thank you. Paul. ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote: That mostly looks good. I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask. The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups. 1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr. On 8/2/2019 3:56 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune ##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune ##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz ##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz ##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz ##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz ##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz ##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz ###-----repeat steps 1-8 for cortical thickness------- ###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir ###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct? Thank you very much. Paul. The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvr1.mtx= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvr2.mtx= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education? On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote: Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2 On 8/1/2019 3:14 PM, miracle ozzoude wrote:External Email - Use Caution Please, can anyone help me with this. Thank you Paul ---------- Forwarded message --------- From: *miracle ozzoude* <miracooloz@gmail.com<mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com<mailto:miracooloz@gmail.com>>> Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>> Hello Experts, I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education). However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions. Thank you. Best, Paul The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14 Input YY1 g2 62 20 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvrgroup1= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvrgroup2= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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11:24 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
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these regions (please see below) came out significant for the voxel-wise corrected map. I want to know their p-values. mri-glmfit-sim doesn't give summary file for voxel-wise corrected map only for cluster-wise map. [image: image.png]
On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
I'm not sure what you are looking for. The voxel-wise analysis is voxel-wise, so there is no summary file for it
On 8/12/2019 11:13 AM, miracle ozzoude wrote:
External Email - Use CautionThanks Doug. Another question, how do i find the p-values for voxel-wise map corrected for multiple comparisons at a voxel (rather than cluster) level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. Best, Paul
On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
The 3 spaces is for left hemi, right hemi, and subcortical, so, if you are using all three then correct for all 3
On 8/7/19 9:26 AM, miracle ozzoude wrote:
External Email - Use CautionGot it. Thanks a lot doug. If i have to correct for multiple comparison in surface based pet analysis and mutlimodal analysis (pet and thickness), should i use --3spaces? Thank you.
best, Paul
On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I think there is still something not right. You should just have one mri_glmfit command for each hemisphere in which the input is ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the same as the first but with a reversed sign, but it is not necessary since we always use unsigned tests and show both signs (but you can still do it). On 8/5/2019 8:14 PM, miracle ozzoude wrote:External Email - Use Caution I think i got it now. Something like this: ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group
mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr) On 8/5/2019 4:39 PM, miracooloz wrote:External Email - Use Caution Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right. Best, Paul. Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu> Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr Yes, that contrast is correct. On 8/5/2019 3:11 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct. Thank you. Paul. ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>wrote:
That mostly looks good. I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask. The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups. 1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr. On 8/2/2019 3:56 PM, miracle ozzoude wrote:> > External Email - Use Caution > > Hello Doug, > > Thanks for answering. Based on your explanation, i > wrote out a series of command needed to execute this. > Please let me know if i made any mistakes/correct. > ##step1 concatenating the 10 amyloid pet volumes files > projected to surface using mri_vol2surf for group1 > mri_concat --f grp1.lhmgxctx --o > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > mri_concat --f grp2.rhmgxctx --o > allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > > ##step2 concatenating the 20 amyloid pet volumes files > projected to surface using mri_vol2surf for group2 > mri_concat --f grp2.lhmgxctx --o > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > mri_concat --f grp2.rhmgxctx --o > allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > > ##step3 smooth on the surface for each hemisphere for > group1 > mri_surf2surf --hemi lh --s fsaverage --sval > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > mri_surf2surf --hemi rh --s fsaverage --sval > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > ##step4 smooth on the surface for each hemisphere for > group2 > mri_surf2surf --hemi lh --s fsaverage --sval > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > mri_surf2surf --hemi rh --s fsaverage --sval > allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > > ##step5 create files of zeros for group1 for each > hemisphere > fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > ##step6 create files of zeros for group2 for each > hemisphere > fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > > ##step7 create pvr files for group1 for each hemisphere > mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > lh.pvr_grp1_pet.nii.gz > mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > rh.pvr_grp1_pet.nii.gz > > ##step8 create pvr files for group2 for each hemisphere > mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > lh.pvr_grp2_pet.nii.gz > mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > rh.pvr_grp2_pet.nii.gz > > ###-----repeat steps 1-8 for cortical thickness------- > > ###run glm-fit for group1 > mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd > project.fsgd dods --c pvr1.mtx --pvr > lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex > --glmdir lh.grp1.pet.thickness.glmdir > mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd > project.fsgd dods --c pvr1.mtx --pvr > rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex > --glmdir rh.grp1.pet.thickness.glmdir > > ###run glm-fit for group2 > mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd > project.fsgd dods --c pvr2.mtx --pvr > lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex > --glmdir lh.grp2.pet.thickness.glmdir > mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd > project.fsgd dods --c pvr2.mtx --pvr > rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex > --glmdir rh.grp2.pet.thickness.glmdir > > My questions. > 1) will my fsgd file contain both groups? > 2) If the answer from question is yes, i should have 2 > contrasts (pvr1.mtx for group1 and pvr2.mtx for > group2). yes/no? > 3) below is a sample of my fsgd file. are the > constrasts correct? > > Thank you very much. > Paul. > The fsgd file lists: >
> GroupDescriptorFile 1 > Title Relationship Amy-thick reg out age and education > Class g1 > Class g2 > Variable Age Education > Input XX1 g1 60 16 > Input YY1 g2 62 20 >
> matrix for group1: > pvr1.mtx= 1 0 0 0 0 0 0 > is there a relationship between amyloid-thickness in
group1 regressing out age
> and education? > matrix for group2: > pvr2.mtx= 0 1 0 0 0 0 0 > is there a relationship between amyloid-thickness in
group2 regressing out age
> and education? > > On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu> wrote: > > Each PVR adds a single column to the design > matrix. In a two group design, this can make it > tricky to set up. Let's say you have 10 of group1 > and 20 of group2. You will need to create two PVR > files, each with 30=10+20 frames. In the first > one, the first 10 frames will be cortical > thickness (or amyloid sampled on the surface) of > group1; the next 20 frames will be all zeros. For > the 2nd PVR, the first 10 frames will be 0s and > the next 20 frames will be the cortical thickness > (or amyloid) for group2. I would start by running > mris_preproc for the two groups separate (so 2 > files, one with 10 frames the other 20 frames). > Then create the file of zeros using > fscalc group2.mgz mul 0 -o group2.zeros.mgz > Then > mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz > Then create the contrast based on the FSGD, but > then add two more numbers, one for PVR1 (which > tests for the within group correlation), and one > for PVR2 > > > On 8/1/2019 3:14 PM, miracle ozzoude wrote: >> >> External Email - Use Caution >> >> Please, can anyone help me with this. >> Thank you >> >> Paul >> >> ---------- Forwarded message --------- >> From: *miracle ozzoude* <miracooloz@gmail.com >> mailto:miracooloz@gmail.com> >> Date: Wed, Jul 31, 2019 at 2:11 PM >> Subject: multimodal analysis (pet and cortical >> thickness relationship) using --pvr >> To: Douglas N Greve >> <freesurfer@nmr.mgh.harvard.edu >> mailto:freesurfer@nmr.mgh.harvard.edu> >> >> >> Hello Experts, >> >> I am performing an analysis looking at the >> relationship between amyloid uptake and cortical >> thickness using --pvr flag in mri_glmfit. I've 2 >> groups and 2 variables (age and education). I >> want to run a within group analysis while >> regressing out age and education (i.e. Within >> group 1, is there a negative relationship between >> amyloid uptake and cortical thickness regressing >> out the effects of age and education). >> >> However, i'm not sure how my pvr contrasts will >> look like. Below are my fsgd and an attempt at >> creating contrasts. Please, can you let me know >> if my contrasts are correct based on my questions. >> >> Thank you. >> >> Best, >> Paul >> >> The fsgd file lists: >>
>> GroupDescriptorFile 1 >> Title Relationship Amy-thick reg out age and
education
>> Class g1 >> Class g2 >> Variable Age Education >> Input XX1 g1 60 16 >> Input XX2 g1 58 14 >> Input YY1 g2 62 20 >> Input YY1 g2 62 20 >>
>> matrix for group1: >> pvrgroup1= 1 0 0 0 0 0 0 >> is there a relationship between amyloid-thickness
in group1 regressing out age
>> and education? >> matrix for group2: >> pvrgroup2= 0 1 0 0 0 0 0 >> is there a relationship between amyloid-thickness
in group2 regressing out age
>> and education? >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
>
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11:30 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
You will have to click on the vertex you are interested in. The value will be -log10(pcorrected) where pcorrected is the corrected p-value
On 8/12/2019 11:24 AM, miracle ozzoude wrote:
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these regions (please see below) came out significant for the voxel-wise corrected map. I want to know their p-values. mri-glmfit-sim doesn't give summary file for voxel-wise corrected map only for cluster-wise map. [image.png]
On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: I'm not sure what you are looking for. The voxel-wise analysis is voxel-wise, so there is no summary file for it
On 8/12/2019 11:13 AM, miracle ozzoude wrote:
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Thanks Doug. Another question, how do i find the p-values for voxel-wise map corrected for multiple comparisons at a voxel (rather than cluster) level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. Best, Paul
On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: The 3 spaces is for left hemi, right hemi, and subcortical, so, if you are using all three then correct for all 3
On 8/7/19 9:26 AM, miracle ozzoude wrote:
External Email - Use CautionGot it. Thanks a lot doug. If i have to correct for multiple comparison in surface based pet analysis and mutlimodal analysis (pet and thickness), should i use --3spaces? Thank you.
best, Paul
On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote:
I think there is still something not right. You should just have one mri_glmfit command for each hemisphere in which the input is ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the same as the first but with a reversed sign, but it is not necessary since we always use unsigned tests and show both signs (but you can still do it). On 8/5/2019 8:14 PM, miracle ozzoude wrote:External Email - Use Caution I think i got it now. Something like this: ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote: It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr) On 8/5/2019 4:39 PM, miracooloz wrote:External Email - Use Caution Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right. Best, Paul. Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr Yes, that contrast is correct. On 8/5/2019 3:11 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks very much for your help. Your assumption was right in that i want to run a group comparison (i.e. test for a difference in amyloid-thickness slopes between the two groups). However, I am having a hard time creating the correct mri_glmfit and contrasts in this case. Based on your advice and searching through the forum (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it another shot below. Please let me know if i am correct. Thank you. Paul. ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote: That mostly looks good. I would suggest is to change your smoothing command to something like mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz The only difference will be that any vertices that are 0 in the input will be excluded (pruned) from the smoothing mask. The mri_glmfit command is not right. That command looks like it is for analyzing each group separately and independently. If that is what you want to do, then you don't need to go through all the extra stuff of creating zero files, etc. I had assumed that you wanted to do some kind of comparison between groups. If so, then you would use a single file with all your data in it (probably what you were using before), and your fsgd file would have both groups. 1) will my fsgd file contain both groups? yes, see above 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? Again, if all you want to do is to test the pvr for each group separately, then you don't need to go through the processes of creating zero files, etc. In any event, if you want to test a pvr, then you need a contrast for it. 3) below is a sample of my fsgd file. are the constrasts correct? hard to say without resolving the questions above. You will need to have a value in the contrast for each pvr. On 8/2/2019 3:56 PM, miracle ozzoude wrote:External Email - Use Caution Hello Doug, Thanks for answering. Based on your explanation, i wrote out a series of command needed to execute this. Please let me know if i made any mistakes/correct. ##step1 concatenating the 10 amyloid pet volumes files projected to surface using mri_vol2surf for group1 mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune ##step2 concatenating the 20 amyloid pet volumes files projected to surface using mri_vol2surf for group2 mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune ##step3 smooth on the surface for each hemisphere for group1 mri_surf2surf --hemi lh --s fsaverage --sval allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz ##step4 smooth on the surface for each hemisphere for group2 mri_surf2surf --hemi lh --s fsaverage --sval allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mri_surf2surf --hemi rh --s fsaverage --sval allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz ##step5 create files of zeros for group1 for each hemisphere fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz ##step6 create files of zeros for group2 for each hemisphere fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz ##step7 create pvr files for group1 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o lh.pvr_grp1_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o rh.pvr_grp1_pet.nii.gz ##step8 create pvr files for group2 for each hemisphere mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o lh.pvr_grp2_pet.nii.gz mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o rh.pvr_grp2_pet.nii.gz ###-----repeat steps 1-8 for cortical thickness------- ###run glm-fit for group1 mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp1.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd project.fsgd dods --c pvr1.mtx --pvr rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp1.pet.thickness.glmdir ###run glm-fit for group2 mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir lh.grp2.pet.thickness.glmdir mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd project.fsgd dods --c pvr2.mtx --pvr rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex --glmdir rh.grp2.pet.thickness.glmdir My questions. 1) will my fsgd file contain both groups? 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx for group1 and pvr2.mtx for group2). yes/no? 3) below is a sample of my fsgd file. are the constrasts correct? Thank you very much. Paul. The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvr1.mtx= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvr2.mtx= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education? On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote: Each PVR adds a single column to the design matrix. In a two group design, this can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2. You will need to create two PVR files, each with 30=10+20 frames. In the first one, the first 10 frames will be cortical thickness (or amyloid sampled on the surface) of group1; the next 20 frames will be all zeros. For the 2nd PVR, the first 10 frames will be 0s and the next 20 frames will be the cortical thickness (or amyloid) for group2. I would start by running mris_preproc for the two groups separate (so 2 files, one with 10 frames the other 20 frames). Then create the file of zeros using fscalc group2.mgz mul 0 -o group2.zeros.mgz Then mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz Then create the contrast based on the FSGD, but then add two more numbers, one for PVR1 (which tests for the within group correlation), and one for PVR2 On 8/1/2019 3:14 PM, miracle ozzoude wrote:External Email - Use Caution Please, can anyone help me with this. Thank you Paul ---------- Forwarded message --------- From: *miracle ozzoude* <miracooloz@gmail.com<mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com<mailto:miracooloz@gmail.com>>> Date: Wed, Jul 31, 2019 at 2:11 PM Subject: multimodal analysis (pet and cortical thickness relationship) using --pvr To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>> Hello Experts, I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education). However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions. Thank you. Best, Paul The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14 Input YY1 g2 62 20 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvrgroup1= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvrgroup2= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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13 Aug
13 Aug
10:17 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
Thanks Doug. My correction for multiple comparison using 10000 permutation and abs has been running for 3days. This is strange because i am using the --bg 10 and it usually takes 1hr to finish without the --pvr. how do i solve this? Below is my mri_glmfit and mri_glmfit-sim commands
mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd dods --C $pvr1 --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf fsaverage lh --cortex \ --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save
mri_glmfit-sim --glmdir ${wholebrain}/lh.pet.thickness.glmdir --perm 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite
On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
You will have to click on the vertex you are interested in. The value will be -log10(pcorrected) where pcorrected is the corrected p-value
On 8/12/2019 11:24 AM, miracle ozzoude wrote:
External Email - Use Cautionthese regions (please see below) came out significant for the voxel-wise corrected map. I want to know their p-values. mri-glmfit-sim doesn't give summary file for voxel-wise corrected map only for cluster-wise map. [image: image.png]
On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
I'm not sure what you are looking for. The voxel-wise analysis is voxel-wise, so there is no summary file for it
On 8/12/2019 11:13 AM, miracle ozzoude wrote:
External Email - Use CautionThanks Doug. Another question, how do i find the p-values for voxel-wise map corrected for multiple comparisons at a voxel (rather than cluster) level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. Best, Paul
On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
The 3 spaces is for left hemi, right hemi, and subcortical, so, if you are using all three then correct for all 3
On 8/7/19 9:26 AM, miracle ozzoude wrote:
External Email - Use CautionGot it. Thanks a lot doug. If i have to correct for multiple comparison in surface based pet analysis and mutlimodal analysis (pet and thickness), should i use --3spaces? Thank you.
best, Paul
On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I think there is still something not right. You should just have one mri_glmfit command for each hemisphere in which the input is ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the same as the first but with a reversed sign, but it is not necessary since we always use unsigned tests and show both signs (but you can still do it). On 8/5/2019 8:14 PM, miracle ozzoude wrote:External Email - Use Caution I think i got it now. Something like this: ## group1 comes first in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group
mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 1 -1 ##group 2 is second in my fsgd file. removing the effects of age and education ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir contrast = 0 0 0 0 0 0 -1 1 On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: It still looks like you are using a group specific input (--y). The input should be a simple file with both groups (same input as you would use without pvr) On 8/5/2019 4:39 PM, miracooloz wrote:External Email - Use Caution Thanks Doug. How about the mri_glmfit commands? Since the contrasts are correct, I think the commands should be right. Best, Paul. Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu> Date: 2019-08-05 15:52 (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr Yes, that contrast is correct. On 8/5/2019 3:11 PM, miracle ozzoude wrote:> > External Email - Use Caution > > Hello Doug, > > Thanks very much for your help. Your assumption was right > in that i want to run a group comparison (i.e. test for a > difference in amyloid-thickness slopes between the two > groups). However, I am having a hard time creating the > correct mri_glmfit and contrasts in this case. Based on > your advice and searching through the forum > (
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
> need 2 PVRs for each hemisphere in the mri_glmfit command. > I gave it another shot below. Please let me know if i am > correct. > > Thank you. > Paul. > > ## group1 comes first in my fsgd file. removing the effects > of age and education > ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for > group 2. > mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd > project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz
\
> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir > mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd > project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz
\
> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir > > contrast = 0 0 0 0 0 0 1 -1 > > ##group 2 is second in my fsgd file. removing the effects > of age and education > ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for > group2 > mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd > project.fsgd dods --c pvr2.mtx --pvr > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex > --glmdir rh.pet.thickness.glmdir > mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd > project.fsgd dods --c pvr2.mtx --pvr > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex > --glmdir rh.pet.thickness.glmdir > > contrast = 0 0 0 0 0 0 -1 1 > > > On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>
wrote:
> > That mostly looks good. > > I would suggest is to change your smoothing command to > something like > mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm > 5 --cortex --prune --i > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > The only difference will be that any vertices that are > 0 in the input will be excluded (pruned) from the > smoothing mask. > > The mri_glmfit command is not right. That command looks > like it is for analyzing each group separately and > independently. If that is what you want to do, then you > don't need to go through all the extra stuff of > creating zero files, etc. I had assumed that you wanted > to do some kind of comparison between groups. If so, > then you would use a single file with all your data in > it (probably what you were using before), and your fsgd > file would have both groups. > > 1) will my fsgd file contain both groups? > yes, see above > 2) If the answer from question is yes, i should have 2 > contrasts (pvr1.mtx for group1 and pvr2.mtx for > group2). yes/no? > Again, if all you want to do is to test the pvr for > each group separately, then you don't need to go > through the processes of creating zero files, etc. In > any event, if you want to test a pvr, then you need a > contrast for it. > 3) below is a sample of my fsgd file. are the > constrasts correct? > hard to say without resolving the questions above. You > will need to have a value in the contrast for each pvr. > > > > On 8/2/2019 3:56 PM, miracle ozzoude wrote: >> >> External Email - Use Caution >> >> Hello Doug, >> >> Thanks for answering. Based on your explanation, i >> wrote out a series of command needed to execute this. >> Please let me know if i made any mistakes/correct. >> ##step1 concatenating the 10 amyloid pet volumes files >> projected to surface using mri_vol2surf for group1 >> mri_concat --f grp1.lhmgxctx --o >> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune >> mri_concat --f grp2.rhmgxctx --o >> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune >> >> ##step2 concatenating the 20 amyloid pet volumes files >> projected to surface using mri_vol2surf for group2 >> mri_concat --f grp2.lhmgxctx --o >> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune >> mri_concat --f grp2.rhmgxctx --o >> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune >> >> ##step3 smooth on the surface for each hemisphere for >> group1 >> mri_surf2surf --hemi lh --s fsaverage --sval >> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >> --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >> mri_surf2surf --hemi rh --s fsaverage --sval >> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >> --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >> >> ##step4 smooth on the surface for each hemisphere for >> group2 >> mri_surf2surf --hemi lh --s fsaverage --sval >> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >> --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz >> mri_surf2surf --hemi rh --s fsaverage --sval >> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >> --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz >> >> ##step5 create files of zeros for group1 for each >> hemisphere >> fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >> fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >> >> ##step6 create files of zeros for group2 for each >> hemisphere >> fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz >> fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz >> >> ##step7 create pvr files for group1 for each hemisphere >> mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o >> lh.pvr_grp1_pet.nii.gz >> mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o >> rh.pvr_grp1_pet.nii.gz >> >> ##step8 create pvr files for group2 for each hemisphere >> mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o >> lh.pvr_grp2_pet.nii.gz >> mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o >> rh.pvr_grp2_pet.nii.gz >> >> ###-----repeat steps 1-8 for cortical thickness------- >> >> ###run glm-fit for group1 >> mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd >> project.fsgd dods --c pvr1.mtx --pvr >> lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex >> --glmdir lh.grp1.pet.thickness.glmdir >> mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd >> project.fsgd dods --c pvr1.mtx --pvr >> rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex >> --glmdir rh.grp1.pet.thickness.glmdir >> >> ###run glm-fit for group2 >> mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd >> project.fsgd dods --c pvr2.mtx --pvr >> lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex >> --glmdir lh.grp2.pet.thickness.glmdir >> mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd >> project.fsgd dods --c pvr2.mtx --pvr >> rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex >> --glmdir rh.grp2.pet.thickness.glmdir >> >> My questions. >> 1) will my fsgd file contain both groups? >> 2) If the answer from question is yes, i should have 2 >> contrasts (pvr1.mtx for group1 and pvr2.mtx for >> group2). yes/no? >> 3) below is a sample of my fsgd file. are the >> constrasts correct? >> >> Thank you very much. >> Paul. >> The fsgd file lists: >>
>> GroupDescriptorFile 1 >> Title Relationship Amy-thick reg out age and education >> Class g1 >> Class g2 >> Variable Age Education >> Input XX1 g1 60 16 >> Input YY1 g2 62 20 >>
>> matrix for group1: >> pvr1.mtx= 1 0 0 0 0 0 0 >> is there a relationship between amyloid-thickness in
group1 regressing out age
>> and education? >> matrix for group2: >> pvr2.mtx= 0 1 0 0 0 0 0 >> is there a relationship between amyloid-thickness in
group2 regressing out age
>> and education? >> >> On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> wrote: >> >> Each PVR adds a single column to the design >> matrix. In a two group design, this can make it >> tricky to set up. Let's say you have 10 of group1 >> and 20 of group2. You will need to create two PVR >> files, each with 30=10+20 frames. In the first >> one, the first 10 frames will be cortical >> thickness (or amyloid sampled on the surface) of >> group1; the next 20 frames will be all zeros. For >> the 2nd PVR, the first 10 frames will be 0s and >> the next 20 frames will be the cortical thickness >> (or amyloid) for group2. I would start by running >> mris_preproc for the two groups separate (so 2 >> files, one with 10 frames the other 20 frames). >> Then create the file of zeros using >> fscalc group2.mgz mul 0 -o group2.zeros.mgz >> Then >> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz >> Then create the contrast based on the FSGD, but >> then add two more numbers, one for PVR1 (which >> tests for the within group correlation), and one >> for PVR2 >> >> >> On 8/1/2019 3:14 PM, miracle ozzoude wrote: >>> >>> External Email - Use Caution >>> >>> Please, can anyone help me with this. >>> Thank you >>> >>> Paul >>> >>> ---------- Forwarded message --------- >>> From: *miracle ozzoude* <miracooloz@gmail.com >>> mailto:miracooloz@gmail.com> >>> Date: Wed, Jul 31, 2019 at 2:11 PM >>> Subject: multimodal analysis (pet and cortical >>> thickness relationship) using --pvr >>> To: Douglas N Greve >>> <freesurfer@nmr.mgh.harvard.edu >>> mailto:freesurfer@nmr.mgh.harvard.edu> >>> >>> >>> Hello Experts, >>> >>> I am performing an analysis looking at the >>> relationship between amyloid uptake and cortical >>> thickness using --pvr flag in mri_glmfit. I've 2 >>> groups and 2 variables (age and education). I >>> want to run a within group analysis while >>> regressing out age and education (i.e. Within >>> group 1, is there a negative relationship between >>> amyloid uptake and cortical thickness regressing >>> out the effects of age and education). >>> >>> However, i'm not sure how my pvr contrasts will >>> look like. Below are my fsgd and an attempt at >>> creating contrasts. Please, can you let me know >>> if my contrasts are correct based on my questions. >>> >>> Thank you. >>> >>> Best, >>> Paul >>> >>> The fsgd file lists: >>>
>>> GroupDescriptorFile 1 >>> Title Relationship Amy-thick reg out age and
education
>>> Class g1 >>> Class g2 >>> Variable Age Education >>> Input XX1 g1 60 16 >>> Input XX2 g1 58 14 >>> Input YY1 g2 62 20 >>> Input YY1 g2 62 20 >>>
>>> matrix for group1: >>> pvrgroup1= 1 0 0 0 0 0 0 >>> is there a relationship between amyloid-thickness
in group1 regressing out age
>>> and education? >>> matrix for group2: >>> pvrgroup2= 0 1 0 0 0 0 0 >>> is there a relationship between amyloid-thickness
in group2 regressing out age
>>> and education? >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >>
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>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
>>
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10:38 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
I don't know that there is much you can do. The PVR is very computationally intensive, and it does not surprise me that it is taking a long time. I don't think you need to do 10k permutations. I would start with 1k. In the output, you will get a confidence interval for the corrected p-value. This will shrink with the number of permutations, but if you're happy with it, no need to do more
On 8/13/19 10:17 AM, miracle ozzoude wrote:
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Thanks Doug. My correction for multiple comparison using 10000 permutation and abs has been running for 3days. This is strange because i am using the --bg 10 and it usually takes 1hr to finish without the --pvr. how do i solve this? Below is my mri_glmfit and mri_glmfit-sim commands
mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd dods --C $pvr1 --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf fsaverage lh --cortex \ --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save
mri_glmfit-sim --glmdir ${wholebrain}/lh.pet.thickness.glmdir --perm 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite
On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
You will have to click on the vertex you are interested in. The value will be -log10(pcorrected) where pcorrected is the corrected p-value On 8/12/2019 11:24 AM, miracle ozzoude wrote:External Email - Use Caution these regions (please see below) came out significant for the voxel-wise corrected map. I want to know their p-values. mri-glmfit-sim doesn't give summary file for voxel-wise corrected map only for cluster-wise map. image.png On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: I'm not sure what you are looking for. The voxel-wise analysis is voxel-wise, so there is no summary file for it On 8/12/2019 11:13 AM, miracle ozzoude wrote:External Email - Use Caution Thanks Doug. Another question, how do i find the p-values for voxel-wise map corrected for multiple comparisons at a voxel (rather than cluster) level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. Best, Paul On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: The 3 spaces is for left hemi, right hemi, and subcortical, so, if you are using all three then correct for all 3 On 8/7/19 9:26 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Got it. Thanks a lot doug. If i have to correct for multiple > comparison in surface based pet analysis and mutlimodal analysis (pet > and thickness), should i use --3spaces? > Thank you. > > best, > Paul > > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I think there is still something not right. You should just have > one mri_glmfit command for each hemisphere in which the input is > ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then > specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz > --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The > second is the same as the first but with a reversed sign, but it > is not necessary since we always use unsigned tests and show both > signs (but you can still do it). > > On 8/5/2019 8:14 PM, miracle ozzoude wrote: >> >> External Email - Use Caution >> >> I think i got it now. Something like this: >> >> ## group1 comes first in my fsgd file. removing the effects of >> age and education >> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. >> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ >> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >> fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir >> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ >> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage >> lh --cortex --glmdir rh.pet.thickness.glmdir >> >> contrast = 0 0 0 0 0 0 1 -1 >> >> ##group 2 is second in my fsgd file. removing the effects of age >> and education >> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 >> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c >> pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir >> rh.pet.thickness.glmdir >> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c >> pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir >> rh.pet.thickness.glmdir >> >> contrast = 0 0 0 0 0 0 -1 1 >> >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >> >> It still looks like you are using a group specific input >> (--y). The input should be a simple file with both groups >> (same input as you would use without pvr) >> >> On 8/5/2019 4:39 PM, miracooloz wrote: >>> >>> External Email - Use Caution >>> >>> Thanks Doug. How about the mri_glmfit commands? Since the >>> contrasts are correct, I think the commands should be right. >>> >>> Best, >>> Paul. >>> >>> >>> >>> Sent from my Samsung Galaxy smartphone. >>> >>> -------- Original message -------- >>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> Date: 2019-08-05 15:52 (GMT-05:00) >>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and >>> cortical thickness relationship) using --pvr >>> >>> Yes, that contrast is correct. >>> >>> On 8/5/2019 3:11 PM, miracle ozzoude wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hello Doug, >>>> >>>> Thanks very much for your help. Your assumption was right >>>> in that i want to run a group comparison (i.e. test for a >>>> difference in amyloid-thickness slopes between the two >>>> groups). However, I am having a hard time creating the >>>> correct mri_glmfit and contrasts in this case. Based on >>>> your advice and searching through the forum >>>> (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i >>>> need 2 PVRs for each hemisphere in the mri_glmfit command. >>>> I gave it another shot below. Please let me know if i am >>>> correct. >>>> >>>> Thank you. >>>> Paul. >>>> >>>> ## group1 comes first in my fsgd file. removing the effects >>>> of age and education >>>> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for >>>> group 2. >>>> mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd >>>> project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ >>>> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>>> fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir >>>> mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd >>>> project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ >>>> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>>> fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir >>>> >>>> contrast = 0 0 0 0 0 0 1 -1 >>>> >>>> ##group 2 is second in my fsgd file. removing the effects >>>> of age and education >>>> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for >>>> group2 >>>> mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd >>>> project.fsgd dods --c pvr2.mtx --pvr >>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex >>>> --glmdir rh.pet.thickness.glmdir >>>> mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd >>>> project.fsgd dods --c pvr2.mtx --pvr >>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex >>>> --glmdir rh.pet.thickness.glmdir >>>> >>>> contrast = 0 0 0 0 0 0 -1 1 >>>> >>>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >>>> >>>> That mostly looks good. >>>> >>>> I would suggest is to change your smoothing command to >>>> something like >>>> mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm >>>> 5 --cortex --prune --i >>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>>> The only difference will be that any vertices that are >>>> 0 in the input will be excluded (pruned) from the >>>> smoothing mask. >>>> >>>> The mri_glmfit command is not right. That command looks >>>> like it is for analyzing each group separately and >>>> independently. If that is what you want to do, then you >>>> don't need to go through all the extra stuff of >>>> creating zero files, etc. I had assumed that you wanted >>>> to do some kind of comparison between groups. If so, >>>> then you would use a single file with all your data in >>>> it (probably what you were using before), and your fsgd >>>> file would have both groups. >>>> >>>> 1) will my fsgd file contain both groups? >>>> yes, see above >>>> 2) If the answer from question is yes, i should have 2 >>>> contrasts (pvr1.mtx for group1 and pvr2.mtx for >>>> group2). yes/no? >>>> Again, if all you want to do is to test the pvr for >>>> each group separately, then you don't need to go >>>> through the processes of creating zero files, etc. In >>>> any event, if you want to test a pvr, then you need a >>>> contrast for it. >>>> 3) below is a sample of my fsgd file. are the >>>> constrasts correct? >>>> hard to say without resolving the questions above. You >>>> will need to have a value in the contrast for each pvr. >>>> >>>> >>>> >>>> On 8/2/2019 3:56 PM, miracle ozzoude wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> Hello Doug, >>>>> >>>>> Thanks for answering. Based on your explanation, i >>>>> wrote out a series of command needed to execute this. >>>>> Please let me know if i made any mistakes/correct. >>>>> ##step1 concatenating the 10 amyloid pet volumes files >>>>> projected to surface using mri_vol2surf for group1 >>>>> mri_concat --f grp1.lhmgxctx --o >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune >>>>> mri_concat --f grp2.rhmgxctx --o >>>>> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune >>>>> >>>>> ##step2 concatenating the 20 amyloid pet volumes files >>>>> projected to surface using mri_vol2surf for group2 >>>>> mri_concat --f grp2.lhmgxctx --o >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune >>>>> mri_concat --f grp2.rhmgxctx --o >>>>> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune >>>>> >>>>> ##step3 smooth on the surface for each hemisphere for >>>>> group1 >>>>> mri_surf2surf --hemi lh --s fsaverage --sval >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>>>> --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>>>> mri_surf2surf --hemi rh --s fsaverage --sval >>>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>>>> --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>>>> >>>>> ##step4 smooth on the surface for each hemisphere for >>>>> group2 >>>>> mri_surf2surf --hemi lh --s fsaverage --sval >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>>>> --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz >>>>> mri_surf2surf --hemi rh --s fsaverage --sval >>>>> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>>>> --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz >>>>> >>>>> ##step5 create files of zeros for group1 for each >>>>> hemisphere >>>>> fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> >>>>> ##step6 create files of zeros for group2 for each >>>>> hemisphere >>>>> fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> >>>>> ##step7 create pvr files for group1 for each hemisphere >>>>> mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o >>>>> lh.pvr_grp1_pet.nii.gz >>>>> mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o >>>>> rh.pvr_grp1_pet.nii.gz >>>>> >>>>> ##step8 create pvr files for group2 for each hemisphere >>>>> mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o >>>>> lh.pvr_grp2_pet.nii.gz >>>>> mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o >>>>> rh.pvr_grp2_pet.nii.gz >>>>> >>>>> ###-----repeat steps 1-8 for cortical thickness------- >>>>> >>>>> ###run glm-fit for group1 >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd >>>>> project.fsgd dods --c pvr1.mtx --pvr >>>>> lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex >>>>> --glmdir lh.grp1.pet.thickness.glmdir >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd >>>>> project.fsgd dods --c pvr1.mtx --pvr >>>>> rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex >>>>> --glmdir rh.grp1.pet.thickness.glmdir >>>>> >>>>> ###run glm-fit for group2 >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd >>>>> project.fsgd dods --c pvr2.mtx --pvr >>>>> lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex >>>>> --glmdir lh.grp2.pet.thickness.glmdir >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd >>>>> project.fsgd dods --c pvr2.mtx --pvr >>>>> rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex >>>>> --glmdir rh.grp2.pet.thickness.glmdir >>>>> >>>>> My questions. >>>>> 1) will my fsgd file contain both groups? >>>>> 2) If the answer from question is yes, i should have 2 >>>>> contrasts (pvr1.mtx for group1 and pvr2.mtx for >>>>> group2). yes/no? >>>>> 3) below is a sample of my fsgd file. are the >>>>> constrasts correct? >>>>> >>>>> Thank you very much. >>>>> Paul. >>>>> The fsgd file lists: >>>>> ------------------------------------------------------------- >>>>> GroupDescriptorFile 1 >>>>> Title Relationship Amy-thick reg out age and education >>>>> Class g1 >>>>> Class g2 >>>>> Variable Age Education >>>>> Input XX1 g1 60 16 >>>>> Input YY1 g2 62 20 >>>>> ------------------------------------------------------------- >>>>> matrix for group1: >>>>> pvr1.mtx= 1 0 0 0 0 0 0 >>>>> is there a relationship between amyloid-thickness in group1 regressing out age >>>>> and education? >>>>> matrix for group2: >>>>> pvr2.mtx= 0 1 0 0 0 0 0 >>>>> is there a relationship between amyloid-thickness in group2 regressing out age >>>>> and education? >>>>> >>>>> On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >>>>> >>>>> Each PVR adds a single column to the design >>>>> matrix. In a two group design, this can make it >>>>> tricky to set up. Let's say you have 10 of group1 >>>>> and 20 of group2. You will need to create two PVR >>>>> files, each with 30=10+20 frames. In the first >>>>> one, the first 10 frames will be cortical >>>>> thickness (or amyloid sampled on the surface) of >>>>> group1; the next 20 frames will be all zeros. For >>>>> the 2nd PVR, the first 10 frames will be 0s and >>>>> the next 20 frames will be the cortical thickness >>>>> (or amyloid) for group2. I would start by running >>>>> mris_preproc for the two groups separate (so 2 >>>>> files, one with 10 frames the other 20 frames). >>>>> Then create the file of zeros using >>>>> fscalc group2.mgz mul 0 -o group2.zeros.mgz >>>>> Then >>>>> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz >>>>> Then create the contrast based on the FSGD, but >>>>> then add two more numbers, one for PVR1 (which >>>>> tests for the within group correlation), and one >>>>> for PVR2 >>>>> >>>>> >>>>> On 8/1/2019 3:14 PM, miracle ozzoude wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Please, can anyone help me with this. >>>>>> Thank you >>>>>> >>>>>> Paul >>>>>> >>>>>> ---------- Forwarded message --------- >>>>>> From: *miracle ozzoude* <miracooloz@gmail.com <mailto:miracooloz@gmail.com> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM >>>>>> Subject: multimodal analysis (pet and cortical >>>>>> thickness relationship) using --pvr >>>>>> To: Douglas N Greve >>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> >>>>>> >>>>>> >>>>>> Hello Experts, >>>>>> >>>>>> I am performing an analysis looking at the >>>>>> relationship between amyloid uptake and cortical >>>>>> thickness using --pvr flag in mri_glmfit. I've 2 >>>>>> groups and 2 variables (age and education). I >>>>>> want to run a within group analysis while >>>>>> regressing out age and education (i.e. Within >>>>>> group 1, is there a negative relationship between >>>>>> amyloid uptake and cortical thickness regressing >>>>>> out the effects of age and education). >>>>>> >>>>>> However, i'm not sure how my pvr contrasts will >>>>>> look like. Below are my fsgd and an attempt at >>>>>> creating contrasts. Please, can you let me know >>>>>> if my contrasts are correct based on my questions. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> Best, >>>>>> Paul >>>>>> >>>>>> The fsgd file lists: >>>>>> ------------------------------------------------------------- >>>>>> GroupDescriptorFile 1 >>>>>> Title Relationship Amy-thick reg out age and education >>>>>> Class g1 >>>>>> Class g2 >>>>>> Variable Age Education >>>>>> Input XX1 g1 60 16 >>>>>> Input XX2 g1 58 14 >>>>>> Input YY1 g2 62 20 >>>>>> �� Input YY1 g2 62 20 >>>>>> ------------------------------------------------------------- >>>>>> matrix for group1: >>>>>> pvrgroup1= 1 0 0 0 0 0 0 >>>>>> is there a relationship between amyloid-thickness in group1 regressing out age >>>>>> and education? >>>>>> matrix for group2: >>>>>> pvrgroup2= 0 1 0 0 0 0 0 >>>>>> is there a relationship between amyloid-thickness in group2 regressing out age >>>>>> and education? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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10:50 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
Thanks a lot doug. I want to use mri_fdr instead of mri_glmfit-sim. How do i get a summary of clusters like mri_glmfit-sim? I searched through the forum and based on previous responses, The advice was to do mri_fdr and then use mri_surfcluster without the fdr option to obtain the summary of cluster. Is this correct? Paul
On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
I don't know that there is much you can do. The PVR is very computationally intensive, and it does not surprise me that it is taking a long time. I don't think you need to do 10k permutations. I would start with 1k. In the output, you will get a confidence interval for the corrected p-value. This will shrink with the number of permutations, but if you're happy with it, no need to do more
On 8/13/19 10:17 AM, miracle ozzoude wrote:
External Email - Use CautionThanks Doug. My correction for multiple comparison using 10000 permutation and abs has been running for 3days. This is strange because i am using the --bg 10 and it usually takes 1hr to finish without the --pvr. how do i solve this? Below is my mri_glmfit and mri_glmfit-sim commands
mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd dods --C $pvr1 --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf fsaverage lh --cortex \ --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save
mri_glmfit-sim --glmdir ${wholebrain}/lh.pet.thickness.glmdir --perm 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite
On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
You will have to click on the vertex you are interested in. The value will be -log10(pcorrected) where pcorrected is the corrected p-value On 8/12/2019 11:24 AM, miracle ozzoude wrote:External Email - Use Caution these regions (please see below) came out significant for the voxel-wise corrected map. I want to know their p-values. mri-glmfit-sim doesn't give summary file for voxel-wise corrected map only for cluster-wise map. image.png On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: I'm not sure what you are looking for. The voxel-wise analysis is voxel-wise, so there is no summary file for it On 8/12/2019 11:13 AM, miracle ozzoude wrote:External Email - Use Caution Thanks Doug. Another question, how do i find the p-values for voxel-wise map corrected for multiple comparisons at a voxel (rather than cluster) level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. Best, Paul On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>wrote:
The 3 spaces is for left hemi, right hemi, and subcortical, so, if you are using all three then correct for all 3 On 8/7/19 9:26 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Got it. Thanks a lot doug. If i have to correct for multiple > comparison in surface based pet analysis and mutlimodal analysis (pet > and thickness), should i use --3spaces? > Thank you. > > best, > Paul > > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I think there is still something not right. You should just have > one mri_glmfit command for each hemisphere in which the input is > ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then > specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz > --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The > second is the same as the first but with a reversed sign, but it > is not necessary since we always use unsigned tests and show both > signs (but you can still do it). > > On 8/5/2019 8:14 PM, miracle ozzoude wrote: >> >> External Email - Use Caution >> >> I think i got it now. Something like this: >> >> ## group1 comes first in my fsgd file. removing the effects of >> age and education >> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. >> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ >> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >> fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir >> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ >> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage >> lh --cortex --glmdir rh.pet.thickness.glmdir >> >> contrast = 0 0 0 0 0 0 1 -1 >> >> ##group 2 is second in my fsgd file. removing the effects of age >> and education >> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 >> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c >> pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir >> rh.pet.thickness.glmdir >> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c >> pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir >> rh.pet.thickness.glmdir >> >> contrast = 0 0 0 0 0 0 -1 1 >> >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >> >> It still looks like you are using a group specific input >> (--y). The input should be a simple file with both groups >> (same input as you would use without pvr) >> >> On 8/5/2019 4:39 PM, miracooloz wrote: >>> >>> External Email - Use Caution >>> >>> Thanks Doug. How about the mri_glmfit commands? Since the >>> contrasts are correct, I think the commands should be right. >>> >>> Best, >>> Paul. >>> >>> >>> >>> Sent from my Samsung Galaxy smartphone. >>> >>> -------- Original message -------- >>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> Date: 2019-08-05 15:52 (GMT-05:00) >>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and >>> cortical thickness relationship) using --pvr >>> >>> Yes, that contrast is correct. >>> >>> On 8/5/2019 3:11 PM, miracle ozzoude wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hello Doug, >>>> >>>> Thanks very much for your help. Your assumption was right >>>> in that i want to run a group comparison (i.e. test for a >>>> difference in amyloid-thickness slopes between the two >>>> groups). However, I am having a hard time creating the >>>> correct mri_glmfit and contrasts in this case. Based on >>>> your advice and searching through the forum >>>> (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
>>>> need 2 PVRs for each hemisphere in the mri_glmfit command. >>>> I gave it another shot below. Please let me know if i am >>>> correct. >>>> >>>> Thank you. >>>> Paul. >>>> >>>> ## group1 comes first in my fsgd file. removing the effects >>>> of age and education >>>> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for >>>> group 2. >>>> mri_glmfit --ylh_pvr_grp1_thickness.mgh --fsgd
>>>> project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ >>>> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>>> fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir >>>> mri_glmfit --y rh_pvr_grp1_thickness.mgh--fsgd
>>>> project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ >>>> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>>> fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir >>>> >>>> contrast = 0 0 0 0 0 0 1 -1 >>>> >>>> ##group 2 is second in my fsgd file. removing the effects >>>> of age and education >>>> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for >>>> group2 >>>> mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd >>>> project.fsgd dods --c pvr2.mtx --pvr >>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex >>>> --glmdir rh.pet.thickness.glmdir >>>> mri_glmfit --y rh_pvr_grp2_thickness.mgh--fsgd
>>>> project.fsgd dods --c pvr2.mtx --pvr >>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex >>>> --glmdir rh.pet.thickness.glmdir >>>> >>>> contrast = 0 0 0 0 0 0 -1 1 >>>> >>>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >>>> >>>> That mostly looks good. >>>> >>>> I would suggest is to change your smoothing command to >>>> something like >>>> mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm >>>> 5 --cortex --prune --i >>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>>> The only difference will be that any vertices that are >>>> 0 in the input will be excluded (pruned) from the >>>> smoothing mask. >>>> >>>> The mri_glmfit command is not right. That command looks >>>> like it is for analyzing each group separately and >>>> independently. If that is what you want to do, then you >>>> don't need to go through all the extra stuff of >>>> creating zero files, etc. I had assumed that you wanted >>>> to do some kind of comparison between groups. If so, >>>> then you would use a single file with all your data in >>>> it (probably what you were using before), and your fsgd >>>> file would have both groups. >>>> >>>> 1) will my fsgd file contain both groups? >>>> yes, see above >>>> 2) If the answer from question is yes, i should have 2 >>>> contrasts (pvr1.mtx for group1 and pvr2.mtx for >>>> group2). yes/no? >>>> Again, if all you want to do is to test the pvr for >>>> each group separately, then you don't need to go >>>> through the processes of creating zero files, etc. In >>>> any event, if you want to test a pvr, then you need a >>>> contrast for it. >>>> 3) below is a sample of my fsgd file. are the >>>> constrasts correct? >>>> hard to say without resolving the questions above. You >>>> will need to have a value in the contrast for each pvr. >>>> >>>> >>>> >>>> On 8/2/2019 3:56 PM, miracle ozzoudewrote:
>>>>> >>>>> External Email - Use Caution >>>>> >>>>> Hello Doug, >>>>> >>>>> Thanks for answering. Based on your explanation, i >>>>> wrote out a series of command needed to execute this. >>>>> Please let me know if i made any mistakes/correct. >>>>> ##step1 concatenating the 10 amyloid pet volumes files >>>>> projected to surface using mri_vol2surf for group1 >>>>> mri_concat --f grp1.lhmgxctx --o >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune >>>>> mri_concat --f grp2.rhmgxctx --o >>>>> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune >>>>> >>>>> ##step2 concatenating the 20 amyloid pet volumes files >>>>> projected to surface using mri_vol2surf for group2 >>>>> mri_concat --f grp2.lhmgxctx --o >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune >>>>> mri_concat --f grp2.rhmgxctx --o >>>>> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune >>>>> >>>>> ##step3 smooth on the surface for each hemisphere for >>>>> group1 >>>>> mri_surf2surf --hemi lh --s fsaverage --sval >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>>>> --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>>>> mri_surf2surf --hemi rh --s fsaverage --sval >>>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>>>> --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>>>> >>>>> ##step4 smooth on the surface for each hemisphere for >>>>> group2 >>>>> mri_surf2surf --hemi lh --s fsaverage --sval >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>>>> --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz >>>>> mri_surf2surf --hemi rh --s fsaverage --sval >>>>> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>>>> --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz >>>>> >>>>> ##step5 create files of zeros for group1 for each >>>>> hemisphere >>>>> fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> >>>>> ##step6 create files of zeros for group2 for each >>>>> hemisphere >>>>> fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> >>>>> ##step7 create pvr files for group1 for each hemisphere >>>>> mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o >>>>> lh.pvr_grp1_pet.nii.gz >>>>> mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o >>>>> rh.pvr_grp1_pet.nii.gz >>>>> >>>>> ##step8 create pvr files for group2 for each hemisphere >>>>> mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o >>>>> lh.pvr_grp2_pet.nii.gz >>>>> mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>>>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o >>>>> rh.pvr_grp2_pet.nii.gz >>>>> >>>>> ###-----repeat steps 1-8 for cortical thickness------- >>>>> >>>>> ###run glm-fit for group1 >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd >>>>> project.fsgd dods --c pvr1.mtx --pvr >>>>> lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex >>>>> --glmdir lh.grp1.pet.thickness.glmdir >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd >>>>> project.fsgd dods --c pvr1.mtx --pvr >>>>> rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex >>>>> --glmdir rh.grp1.pet.thickness.glmdir >>>>> >>>>> ###run glm-fit for group2 >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd >>>>> project.fsgd dods --c pvr2.mtx --pvr >>>>> lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex >>>>> --glmdir lh.grp2.pet.thickness.glmdir >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd >>>>> project.fsgd dods --c pvr2.mtx --pvr >>>>> rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex >>>>> --glmdir rh.grp2.pet.thickness.glmdir >>>>> >>>>> My questions. >>>>> 1) will my fsgd file contain both groups? >>>>> 2) If the answer from question is yes, i should have 2 >>>>> contrasts (pvr1.mtx for group1 and pvr2.mtx for >>>>> group2). yes/no? >>>>> 3) below is a sample of my fsgd file. are the >>>>> constrasts correct? >>>>> >>>>> Thank you very much. >>>>> Paul. >>>>> The fsgd file lists: >>>>>
>>>>> GroupDescriptorFile 1 >>>>> Title Relationship Amy-thick reg out age and education >>>>> Class g1 >>>>> Class g2 >>>>> Variable Age Education >>>>> Input XX1 g1 60 16 >>>>> Input YY1 g2 62 20 >>>>>
>>>>> matrix for group1: >>>>> pvr1.mtx= 1 0 0 0 0 0 0 >>>>> is there a relationship between amyloid-thickness in group1 regressing out age >>>>> and education? >>>>> matrix for group2: >>>>> pvr2.mtx= 0 1 0 0 0 0 0 >>>>> is there a relationship between amyloid-thickness in group2 regressing out age >>>>> and education? >>>>> >>>>> On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >>>>> >>>>> Each PVR adds a single column to the design >>>>> matrix. In a two group design, this can make it >>>>> tricky to set up. Let's say you have 10 of group1 >>>>> and 20 of group2. You will need to create two PVR >>>>> files, each with 30=10+20 frames. In the first >>>>> one, the first 10 frames will be cortical >>>>> thickness (or amyloid sampled on the surface) of >>>>> group1; the next 20 frames will be all zeros. For >>>>> the 2nd PVR, the first 10 frames will be 0s and >>>>> the next 20 frames will be the cortical thickness >>>>> (or amyloid) for group2. I would start by running >>>>> mris_preproc for the two groups separate (so 2 >>>>> files, one with 10 frames the other 20 frames). >>>>> Then create the file of zeros using >>>>> fscalc group2.mgz mul 0 -o group2.zeros.mgz >>>>> Then >>>>> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz >>>>> Then create the contrast based on the FSGD, but >>>>> then add two more numbers, one for PVR1 (which >>>>> tests for the within group correlation), and one >>>>> for PVR2 >>>>> >>>>> >>>>> On 8/1/2019 3:14 PM, miracle ozzoude wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Please, can anyone help me with this. >>>>>> Thank you >>>>>> >>>>>> Paul >>>>>> >>>>>> ---------- Forwarded message --------- >>>>>> From: *miracle ozzoude* <miracooloz@gmail.com <mailto:miracooloz@gmail.com> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM >>>>>> Subject: multimodal analysis (pet and cortical >>>>>> thickness relationship) using --pvr >>>>>> To: Douglas N Greve >>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> >>>>>> >>>>>> >>>>>> Hello Experts, >>>>>> >>>>>> I am performing an analysis looking at the >>>>>> relationship between amyloid uptake and cortical >>>>>> thickness using --pvr flag in mri_glmfit. I've 2 >>>>>> groups and 2 variables (age and education). I >>>>>> want to run a within group analysis while >>>>>> regressing out age and education (i.e. Within >>>>>> group 1, is there a negative relationship between >>>>>> amyloid uptake and cortical thickness regressing >>>>>> out the effects of age and education). >>>>>> >>>>>> However, i'm not sure how my pvr contrasts will >>>>>> look like. Below are my fsgd and an attempt at >>>>>> creating contrasts. Please, can you let me know >>>>>> if my contrasts are correct based on my questions. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> Best, >>>>>> Paul >>>>>> >>>>>> The fsgd file lists: >>>>>>
>>>>>> GroupDescriptorFile 1 >>>>>> Title Relationship Amy-thick reg out age and education >>>>>> Class g1 >>>>>> Class g2 >>>>>> Variable Age Education >>>>>> Input XX1 g1 60 16 >>>>>> Input XX2 g1 58 14 >>>>>> Input YY1 g2 62 20 >>>>>> �� Input YY1 g2 62 20 >>>>>>
>>>>>> matrix for group1: >>>>>> pvrgroup1= 1 0 0 0 0 0 0 >>>>>> is there a relationship between amyloid-thickness in group1 regressing out age >>>>>> and education? >>>>>> matrix for group2: >>>>>> pvrgroup2= 0 1 0 0 0 0 0 >>>>>> is there a relationship between amyloid-thickness in group2 regressing out age >>>>>> and education? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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10:58 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
You can use mri_surfcluster. That actually has an --fdr flag, so you should not need to run mri_fdr. When you use --fdr, you do not use --thmin. Use --sum to get the summary file
On 8/13/19 10:50 AM, miracle ozzoude wrote:
External Email - Use Caution
Thanks a lot doug. I want to use mri_fdr instead of mri_glmfit-sim. How do i get a summary of clusters like mri_glmfit-sim? I searched through the forum and based on previous responses, The advice was to do mri_fdr and then use mri_surfcluster without the fdr option to obtain the summary of cluster. Is this correct? Paul
On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I don't know that there is much you can do. The PVR is very computationally intensive, and it does not surprise me that it is taking a long time. I don't think you need to do 10k permutations. I would start with 1k. In the output, you will get a confidence interval for the corrected p-value. This will shrink with the number of permutations, but if you're happy with it, no need to do more On 8/13/19 10:17 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Thanks Doug. My correction for multiple comparison using 10000 > permutation and abs has been running for 3days. This is strange > because i am using the --bg 10 and it usually takes 1hr to finish > without the --pvr. how do i solve this? > Below is my mri_glmfit and mri_glmfit-sim commands > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd dods --C $pvr1 > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf fsaverage lh > --cortex \ > --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save > > mri_glmfit-sim --glmdir ${wholebrain}/lh.pet.thickness.glmdir --perm > 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > You will have to click on the vertex you are interested in. The > value will be -log10(pcorrected) where pcorrected is the corrected > p-value > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: >> >> External Email - Use Caution >> >> these regions (please see below) came out significant for the >> voxel-wise corrected map. I want to know their p-values. >> mri-glmfit-sim doesn't give summary file for voxel-wise corrected >> map only for cluster-wise map. >> image.png >> >> On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >> >> I'm not sure what you are looking for. The voxel-wise >> analysis is voxel-wise, so there is no summary file for it >> >> On 8/12/2019 11:13 AM, miracle ozzoude wrote: >>> >>> External Email - Use Caution >>> >>> Thanks Doug. Another question, how do i find the p-values >>> for voxel-wise map corrected for multiple comparisons at a >>> voxel (rather than cluster) level >>> (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. >>> Best, >>> Paul >>> >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >>> >>> The 3 spaces is for left hemi, right hemi, and >>> subcortical, so, if you >>> are using all three then correct for all 3 >>> >>> On 8/7/19 9:26 AM, miracle ozzoude wrote: >>> > >>> > External Email - Use Caution >>> > >>> > Got it. Thanks a lot doug. If i have to correct for >>> multiple >>> > comparison in surface based pet analysis and >>> mutlimodal analysis (pet >>> > and thickness), should i use --3spaces? >>> > Thank you. >>> > >>> > best, >>> > Paul >>> > >>> > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> > >>> > I think there is still something not right. You >>> should just have >>> > one mri_glmfit command for each hemisphere in >>> which the input is >>> > ?h.thickness.15.mgh, the fsgdfile is project.fsgd, >>> you then >>> > specify the pvrs for both groups (--pvr >>> ?h.pvr_grp1_pet.nii.gz >>> > --pvr ?h.pvr_grp2_pet.niigz) and then use that >>> first contrast. The >>> > second is the same as the first but with a >>> reversed sign, but it >>> > is not necessary since we always use unsigned >>> tests and show both >>> > signs (but you can still do it). >>> > >>> > On 8/5/2019 8:14 PM, miracle ozzoude wrote: >>> >> >>> >> External Email - Use Caution >>> >> >>> >> I think i got it now. Something like this: >>> >> >>> >> ## group1 comes first in my fsgd file. removing >>> the effects of >>> >> age and education >>> >> ##amyloid-thickness. first pet pvr = 1 for group1 >>> and 0 for group 2. >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ >>> >> --pvr >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >> fsaverage lh --cortex --glmdir >>> lh.pet.thickness.glmdir >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ >>> >> --pvr >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage >>> >> lh --cortex --glmdir rh.pet.thickness.glmdir >>> >> >>> >> contrast = 0 0 0 0 0 0 1 -1 >>> >> >>> >> ##group 2 is second in my fsgd file. removing the >>> effects of age >>> >> and education >>> >> ##amyloid-thickness. first pet pvr = 0 for group1 >>> and 1 for group2 >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr2.mtx --pvr >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh >>> --cortex --glmdir >>> >> rh.pet.thickness.glmdir >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr2.mtx --pvr >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh >>> --cortex --glmdir >>> >> rh.pet.thickness.glmdir >>> >> >>> >> contrast = 0 0 0 0 0 0 -1 1 >>> >> >>> >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas >>> N.,Ph.D. >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >> >>> >> It still looks like you are using a group >>> specific input >>> >> (--y). The input should be a simple file with >>> both groups >>> >> (same input as you would use without pvr) >>> >> >>> >> On 8/5/2019 4:39 PM, miracooloz wrote: >>> >>> >>> >>> External Email - Use Caution >>> >>> >>> >>> Thanks Doug. How about the mri_glmfit >>> commands? Since the >>> >>> contrasts are correct, I think the commands >>> should be right. >>> >>> >>> >>> Best, >>> >>> Paul. >>> >>> >>> >>> >>> >>> >>> >>> Sent from my Samsung Galaxy smartphone. >>> >>> >>> >>> -------- Original message -------- >>> >>> From: "Greve, Douglas N.,Ph.D." >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> >>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> >>> >>> Date: 2019-08-05 15:52 (GMT-05:00) >>> >>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> >>> >>> Subject: Re: [Freesurfer] Fwd: multimodal >>> analysis (pet and >>> >>> cortical thickness relationship) using --pvr >>> >>> >>> >>> Yes, that contrast is correct. >>> >>> >>> >>> On 8/5/2019 3:11 PM, miracle ozzoude wrote: >>> >>>> >>> >>>> External Email - Use Caution >>> >>>> >>> >>>> Hello Doug, >>> >>>> >>> >>>> Thanks very much for your help. Your >>> assumption was right >>> >>>> in that i want to run a group comparison >>> (i.e. test for a >>> >>>> difference in amyloid-thickness slopes >>> between the two >>> >>>> groups). However, I am having a hard time >>> creating the >>> >>>> correct mri_glmfit and contrasts in this >>> case. Based on >>> >>>> your advice and searching through the forum >>> >>>> >>> (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i >>> >>>> need 2 PVRs for each hemisphere in the >>> mri_glmfit command. >>> >>>> I gave it another shot below. Please let me >>> know if i am >>> >>>> correct. >>> >>>> >>> >>>> Thank you. >>> >>>> Paul. >>> >>>> >>> >>>> ## group1 comes first in my fsgd file. >>> removing the effects >>> >>>> of age and education >>> >>>> ##amyloid-thickness. first pet pvr = 1 for >>> group1 and 0 for >>> >>>> group 2. >>> >>>> mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr1.mtx --pvr >>> lh.pvr_grp1_pet.nii.gz \ >>> >>>> --pvr >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >>>> fsaverage lh --cortex --glmdir >>> lh.pet.thickness.glmdir >>> >>>> mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr1.mtx --pvr >>> rh.pvr_grp1_pet.nii.gz \ >>> >>>> --pvr >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >>>> fsaverage lh --cortex --glmdir >>> rh.pet.thickness.glmdir >>> >>>> >>> >>>> contrast = 0 0 0 0 0 0 1 -1 >>> >>>> >>> >>>> ##group 2 is second in my fsgd file. >>> removing the effects >>> >>>> of age and education >>> >>>> ##amyloid-thickness. first pet pvr = 0 for >>> group1 and 1 for >>> >>>> group2 >>> >>>> mri_glmfit --y >>> lh_pvr_grp2_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf >>> fsaverage lh --cortex >>> >>>> --glmdir rh.pet.thickness.glmdir >>> >>>> mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf >>> fsaverage lh --cortex >>> >>>> --glmdir rh.pet.thickness.glmdir >>> >>>> >>> >>>> contrast = 0 0 0 0 0 0 -1 1 >>> >>>> >>> >>>> >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, >>> Douglas N.,Ph.D. >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >>>> >>> >>>> That mostly looks good. >>> >>>> >>> >>>> I would suggest is to change your >>> smoothing command to >>> >>>> something like >>> >>>> mris_fwhm --smooth-only --s fsaverage >>> --hemi lh --fwhm >>> >>>> 5 --cortex --prune --i >>> >>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>> The only difference will be that any >>> vertices that are >>> >>>> 0 in the input will be excluded >>> (pruned) from the >>> >>>> smoothing mask. >>> >>>> >>> >>>> The mri_glmfit command is not right. >>> That command looks >>> >>>> like it is for analyzing each group >>> separately and >>> >>>> independently. If that is what you want >>> to do, then you >>> >>>> don't need to go through all the extra >>> stuff of >>> >>>> creating zero files, etc. I had assumed >>> that you wanted >>> >>>> to do some kind of comparison between >>> groups. If so, >>> >>>> then you would use a single file with >>> all your data in >>> >>>> it (probably what you were using >>> before), and your fsgd >>> >>>> file would have both groups. >>> >>>> >>> >>>> 1) will my fsgd file contain both groups? >>> >>>> yes, see above >>> >>>> 2) If the answer from question is yes, >>> i should have 2 >>> >>>> contrasts (pvr1.mtx for group1 and >>> pvr2.mtx for >>> >>>> group2). yes/no? >>> >>>> Again, if all you want to do is to test >>> the pvr for >>> >>>> each group separately, then you don't >>> need to go >>> >>>> through the processes of creating zero >>> files, etc. In >>> >>>> any event, if you want to test a pvr, >>> then you need a >>> >>>> contrast for it. >>> >>>> 3) below is a sample of my fsgd file. >>> are the >>> >>>> constrasts correct? >>> >>>> hard to say without resolving the >>> questions above. You >>> >>>> will need to have a value in the >>> contrast for each pvr. >>> >>>> >>> >>>> >>> >>>> >>> >>>> On 8/2/2019 3:56 PM, miracle ozzoude wrote: >>> >>>>> >>> >>>>> External Email - Use Caution >>> >>>>> >>> >>>>> Hello Doug, >>> >>>>> >>> >>>>> Thanks for answering. Based on your >>> explanation, i >>> >>>>> wrote out a series of command needed >>> to execute this. >>> >>>>> Please let me know if i made any >>> mistakes/correct. >>> >>>>> ##step1 concatenating the 10 amyloid >>> pet volumes files >>> >>>>> projected to surface using >>> mri_vol2surf for group1 >>> >>>>> mri_concat --f grp1.lhmgxctx --o >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune >>> >>>>> mri_concat --f grp2.rhmgxctx --o >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune >>> >>>>> >>> >>>>> ##step2 concatenating the 20 amyloid >>> pet volumes files >>> >>>>> projected to surface using >>> mri_vol2surf for group2 >>> >>>>> mri_concat --f grp2.lhmgxctx --o >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune >>> >>>>> mri_concat --f grp2.rhmgxctx --o >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune >>> >>>>> >>> >>>>> ##step3 smooth on the surface for each >>> hemisphere for >>> >>>>> group1 >>> >>>>> mri_surf2surf --hemi lh --s fsaverage >>> --sval >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>> >>>>> --cortex --tval >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> mri_surf2surf --hemi rh --s fsaverage >>> --sval >>> >>>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>> >>>>> --cortex --tval >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> >>> >>>>> ##step4 smooth on the surface for each >>> hemisphere for >>> >>>>> group2 >>> >>>>> mri_surf2surf --hemi lh --s fsaverage >>> --sval >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>> >>>>> --cortex --tval >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> mri_surf2surf --hemi rh --s fsaverage >>> --sval >>> >>>>> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>> >>>>> --cortex --tval >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> >>> >>>>> ##step5 create files of zeros for >>> group1 for each >>> >>>>> hemisphere >>> >>>>> fscalc >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> fscalc >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> >>> >>>>> ##step6 create files of zeros for >>> group2 for each >>> >>>>> hemisphere >>> >>>>> fscalc >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> fscalc >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> >>> >>>>> ##step7 create pvr files for group1 >>> for each hemisphere >>> >>>>> mri_concat >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o >>> >>>>> lh.pvr_grp1_pet.nii.gz >>> >>>>> mri_concat >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o >>> >>>>> rh.pvr_grp1_pet.nii.gz >>> >>>>> >>> >>>>> ##step8 create pvr files for group2 >>> for each hemisphere >>> >>>>> mri_concat >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o >>> >>>>> lh.pvr_grp2_pet.nii.gz >>> >>>>> mri_concat >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o >>> >>>>> rh.pvr_grp2_pet.nii.gz >>> >>>>> >>> >>>>> ###-----repeat steps 1-8 for cortical >>> thickness------- >>> >>>>> >>> >>>>> ###run glm-fit for group1 >>> >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr >>> >>>>> lh_pvr_grp1_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir lh.grp1.pet.thickness.glmdir >>> >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr >>> >>>>> rh_pvr_grp1_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir rh.grp1.pet.thickness.glmdir >>> >>>>> >>> >>>>> ###run glm-fit for group2 >>> >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>>> lh_pvr_grp2_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir lh.grp2.pet.thickness.glmdir >>> >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>>> rh_pvr_grp2_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir rh.grp2.pet.thickness.glmdir >>> >>>>> >>> >>>>> My questions. >>> >>>>> 1) will my fsgd file contain both groups? >>> >>>>> 2) If the answer from question is yes, >>> i should have 2 >>> >>>>> contrasts (pvr1.mtx for group1 and >>> pvr2.mtx for >>> >>>>> group2). yes/no? >>> >>>>> 3) below is a sample of my fsgd file. >>> are the >>> >>>>> constrasts correct? >>> >>>>> >>> >>>>> Thank you very much. >>> >>>>> Paul. >>> >>>>> The fsgd file lists: >>> >>>>> >>> ------------------------------------------------------------- >>> >>>>> GroupDescriptorFile 1 >>> >>>>> Title Relationship Amy-thick reg out >>> age and education >>> >>>>> Class g1 >>> >>>>> Class g2 >>> >>>>> Variable Age Education >>> >>>>> Input XX1 g1 60 16 >>> >>>>> Input YY1 g2 62 20 >>> >>>>> >>> ------------------------------------------------------------- >>> >>>>> matrix for group1: >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 >>> >>>>> is there a relationship between >>> amyloid-thickness in group1 regressing out age >>> >>>>> and education? >>> >>>>> matrix for group2: >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 >>> >>>>> is there a relationship between >>> amyloid-thickness in group2 regressing out age >>> >>>>> and education? >>> >>>>> >>> >>>>> On Thu, Aug 1, 2019 at 9:44 PM Greve, >>> Douglas N.,Ph.D. >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >>>>> >>> >>>>> Each PVR adds a single column to >>> the design >>> >>>>> matrix. In a two group design, >>> this can make it >>> >>>>> tricky to set up. Let's say you >>> have 10 of group1 >>> >>>>> and 20 of group2. You will need to >>> create two PVR >>> >>>>> files, each with 30=10+20 frames. >>> In the first >>> >>>>> one, the first 10 frames will be >>> cortical >>> >>>>> thickness (or amyloid sampled on >>> the surface) of >>> >>>>> group1; the next 20 frames will be >>> all zeros. For >>> >>>>> the 2nd PVR, the first 10 frames >>> will be 0s and >>> >>>>> the next 20 frames will be the >>> cortical thickness >>> >>>>> (or amyloid) for group2. I would >>> start by running >>> >>>>> mris_preproc for the two groups separate (so 2 >>> >>>>> files, one with 10 frames the >>> other 20 frames). >>> >>>>> Then create the file of zeros using >>> >>>>> fscalc group2.mgz mul 0 -o >>> group2.zeros.mgz >>> >>>>> Then >>> >>>>> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz >>> >>>>> Then create the contrast based on >>> the FSGD, but >>> >>>>> then add two more numbers, one for >>> PVR1 (which >>> >>>>> tests for the within group >>> correlation), and one >>> >>>>> for PVR2 >>> >>>>> >>> >>>>> >>> >>>>> On 8/1/2019 3:14 PM, miracle >>> ozzoude wrote: >>> >>>>>> >>> >>>>>> External Email - Use Caution >>> >>>>>> >>> >>>>>> Please, can anyone help me with this. >>> >>>>>> Thank you >>> >>>>>> >>> >>>>>> Paul >>> >>>>>> >>> >>>>>> ---------- Forwarded message --------- >>> >>>>>> From: *miracle ozzoude* >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM >>> >>>>>> Subject: multimodal analysis (pet and cortical >>> >>>>>> thickness relationship) using --pvr >>> >>>>>> To: Douglas N Greve >>> >>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> Hello Experts, >>> >>>>>> >>> >>>>>> I am performing an analysis >>> looking at the >>> >>>>>> relationship between amyloid uptake and cortical >>> >>>>>> thickness using --pvr flag in mri_glmfit. I've 2 >>> >>>>>> groups and 2 variables (age and education). I >>> >>>>>> want to run a within group >>> analysis while >>> >>>>>> regressing out age and education (i.e. Within >>> >>>>>> group 1, is there a negative >>> relationship between >>> >>>>>> amyloid uptake and cortical thickness regressing >>> >>>>>> out the effects of age and >>> education). >>> >>>>>> >>> >>>>>> However, i'm not sure how my pvr contrasts will >>> >>>>>> look like. Below are my fsgd and >>> an attempt at >>> >>>>>> creating contrasts. Please, can you let me know >>> >>>>>> if my contrasts are correct based >>> on my questions. >>> >>>>>> >>> >>>>>> Thank you. >>> >>>>>> >>> >>>>>> Best, >>> >>>>>> Paul >>> >>>>>> >>> >>>>>> The fsgd file lists: >>> >>>>>> >>> ------------------------------------------------------------- >>> >>>>>> GroupDescriptorFile 1 >>> >>>>>> Title Relationship Amy-thick reg >>> out age and education >>> >>>>>> Class g1 >>> >>>>>> Class g2 >>> >>>>>> Variable Age Education >>> >>>>>> Input XX1 g1 60 16 >>> >>>>>> Input XX2 g1 58 14 >>> >>>>>> Input YY1 g2 62 20 >>> >>>>>> �� Input YY1 g2 62 20 >>> >>>>>> >>> ------------------------------------------------------------- >>> >>>>>> matrix for group1: >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 >>> >>>>>> is there a relationship between >>> amyloid-thickness in group1 regressing out age >>> >>>>>> and education? >>> >>>>>> matrix for group2: >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 >>> >>>>>> is there a relationship between >>> amyloid-thickness in group2 regressing out age >>> >>>>>> and education? >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> _______________________________________________ >>> >>>>>> Freesurfer mailing list >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> >>>>>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>>> >>> >>>>> _______________________________________________ >>> >>>>> Freesurfer mailing list >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu 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11 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
Awesome. thanks a lot for your help. I appreciate it.
Best, Paul
On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
You can use mri_surfcluster. That actually has an --fdr flag, so you should not need to run mri_fdr. When you use --fdr, you do not use --thmin. Use --sum to get the summary file
On 8/13/19 10:50 AM, miracle ozzoude wrote:
External Email - Use CautionThanks a lot doug. I want to use mri_fdr instead of mri_glmfit-sim. How do i get a summary of clusters like mri_glmfit-sim? I searched through the forum and based on previous responses, The advice was to do mri_fdr and then use mri_surfcluster without the fdr option to obtain the summary of cluster. Is this correct? Paul
On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I don't know that there is much you can do. The PVR is very computationally intensive, and it does not surprise me that it is taking a long time. I don't think you need to do 10k permutations. I would start with 1k. In the output, you will get a confidence interval for the corrected p-value. This will shrink with the number of permutations, but if you're happy with it, no need to do more On 8/13/19 10:17 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Thanks Doug. My correction for multiple comparison using 10000 > permutation and abs has been running for 3days. This is strange > because i am using the --bg 10 and it usually takes 1hr to finish > without the --pvr. how do i solve this? > Below is my mri_glmfit and mri_glmfit-sim commands > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd dods --C $pvr1 > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf fsaverage lh > --cortex \ > --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save > > mri_glmfit-sim --glmdir ${wholebrain}/lh.pet.thickness.glmdir --perm > 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > You will have to click on the vertex you are interested in. The > value will be -log10(pcorrected) where pcorrected is the corrected > p-value > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: >> >> External Email - Use Caution >> >> these regions (please see below) came out significant for the >> voxel-wise corrected map. I want to know their p-values. >> mri-glmfit-sim doesn't give summary file for voxel-wise corrected >> map only for cluster-wise map. >> image.png >> >> On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >> >> I'm not sure what you are looking for. The voxel-wise >> analysis is voxel-wise, so there is no summary file for it >> >> On 8/12/2019 11:13 AM, miracle ozzoude wrote: >>> >>> External Email - Use Caution >>> >>> Thanks Doug. Another question, how do i find the p-values >>> for voxel-wise map corrected for multiple comparisons ata
>>> voxel (rather than cluster) level >>> (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. >>> Best, >>> Paul >>> >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >>> >>> The 3 spaces is for left hemi, right hemi, and >>> subcortical, so, if you >>> are using all three then correct for all 3 >>> >>> On 8/7/19 9:26 AM, miracle ozzoude wrote: >>> > >>> > External Email - Use Caution >>> > >>> > Got it. Thanks a lot doug. If i have to correct for >>> multiple >>> > comparison in surface based pet analysis and >>> mutlimodal analysis (pet >>> > and thickness), should i use --3spaces? >>> > Thank you. >>> > >>> > best, >>> > Paul >>> > >>> > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> > >>> > I think there is still something not right. You >>> should just have >>> > one mri_glmfit command for each hemisphere in >>> which the input is >>> > ?h.thickness.15.mgh, the fsgdfile is project.fsgd, >>> you then >>> > specify the pvrs for both groups (--pvr >>> ?h.pvr_grp1_pet.nii.gz >>> > --pvr ?h.pvr_grp2_pet.niigz) and then use that >>> first contrast. The >>> > second is the same as the first but with a >>> reversed sign, but it >>> > is not necessary since we always use unsigned >>> tests and show both >>> > signs (but you can still do it). >>> > >>> > On 8/5/2019 8:14 PM, miracle ozzoude wrote: >>> >> >>> >> External Email - Use Caution >>> >> >>> >> I think i got it now. Something like this: >>> >> >>> >> ## group1 comes first in my fsgd file.removing
>>> the effects of >>> >> age and education >>> >> ##amyloid-thickness. first pet pvr = 1 for group1 >>> and 0 for group 2. >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ >>> >> --pvr >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >> fsaverage lh --cortex --glmdir >>> lh.pet.thickness.glmdir >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ >>> >> --pvr >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage >>> >> lh --cortex --glmdir rh.pet.thickness.glmdir >>> >> >>> >> contrast = 0 0 0 0 0 0 1 -1 >>> >> >>> >> ##group 2 is second in my fsgd file. removing the >>> effects of age >>> >> and education >>> >> ##amyloid-thickness. first pet pvr = 0 for group1 >>> and 1 for group2 >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr2.mtx --pvr >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaveragelh
>>> --cortex --glmdir >>> >> rh.pet.thickness.glmdir >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr2.mtx --pvr >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaveragelh
>>> --cortex --glmdir >>> >> rh.pet.thickness.glmdir >>> >> >>> >> contrast = 0 0 0 0 0 0 -1 1 >>> >> >>> >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas >>> N.,Ph.D. >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >> >>> >> It still looks like you are using a group >>> specific input >>> >> (--y). The input should be a simple file with >>> both groups >>> >> (same input as you would use without pvr) >>> >> >>> >> On 8/5/2019 4:39 PM, miracooloz wrote: >>> >>> >>> >>> External Email - Use Caution >>> >>> >>> >>> Thanks Doug. How about the mri_glmfit >>> commands? Since the >>> >>> contrasts are correct, I think the commands >>> should be right. >>> >>> >>> >>> Best, >>> >>> Paul. >>> >>> >>> >>> >>> >>> >>> >>> Sent from my Samsung Galaxy smartphone. >>> >>> >>> >>> -------- Original message -------- >>> >>> From: "Greve, Douglas N.,Ph.D." >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> >>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> >>> >>> Date: 2019-08-05 15:52 (GMT-05:00) >>> >>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> >>> >>> Subject: Re: [Freesurfer] Fwd: multimodal >>> analysis (pet and >>> >>> cortical thickness relationship) using --pvr >>> >>> >>> >>> Yes, that contrast is correct. >>> >>> >>> >>> On 8/5/2019 3:11 PM, miracle ozzoude wrote: >>> >>>> >>> >>>> External Email - Use Caution >>> >>>> >>> >>>> Hello Doug, >>> >>>> >>> >>>> Thanks very much for your help. Your >>> assumption was right >>> >>>> in that i want to run a group comparison >>> (i.e. test for a >>> >>>> difference in amyloid-thickness slopes >>> between the two >>> >>>> groups). However, I am having a hardtime
>>> creating the >>> >>>> correct mri_glmfit and contrasts in this >>> case. Based on >>> >>>> your advice and searching through the forum >>> >>>> >>> (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
>>> >>>> need 2 PVRs for each hemisphere in the >>> mri_glmfit command. >>> >>>> I gave it another shot below. Please let me >>> know if i am >>> >>>> correct. >>> >>>> >>> >>>> Thank you. >>> >>>> Paul. >>> >>>> >>> >>>> ## group1 comes first in my fsgd file. >>> removing the effects >>> >>>> of age and education >>> >>>> ##amyloid-thickness. first pet pvr = 1 for >>> group1 and 0 for >>> >>>> group 2. >>> >>>> mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr1.mtx --pvr >>> lh.pvr_grp1_pet.nii.gz \ >>> >>>> --pvr >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >>>> fsaverage lh --cortex --glmdir >>> lh.pet.thickness.glmdir >>> >>>> mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr1.mtx --pvr >>> rh.pvr_grp1_pet.nii.gz \ >>> >>>> --pvr >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >>>> fsaverage lh --cortex --glmdir >>> rh.pet.thickness.glmdir >>> >>>> >>> >>>> contrast = 0 0 0 0 0 0 1 -1 >>> >>>> >>> >>>> ##group 2 is second in my fsgd file. >>> removing the effects >>> >>>> of age and education >>> >>>> ##amyloid-thickness. first pet pvr = 0 for >>> group1 and 1 for >>> >>>> group2 >>> >>>> mri_glmfit --y >>> lh_pvr_grp2_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf >>> fsaverage lh --cortex >>> >>>> --glmdir rh.pet.thickness.glmdir >>> >>>> mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf >>> fsaverage lh --cortex >>> >>>> --glmdir rh.pet.thickness.glmdir >>> >>>> >>> >>>> contrast = 0 0 0 0 0 0 -1 1 >>> >>>> >>> >>>> >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, >>> Douglas N.,Ph.D. >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >>>> >>> >>>> That mostly looks good. >>> >>>> >>> >>>> I would suggest is to change your >>> smoothing command to >>> >>>> something like >>> >>>> mris_fwhm --smooth-only --s fsaverage >>> --hemi lh --fwhm >>> >>>> 5 --cortex --prune --i >>> >>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>> The only difference will be that any >>> vertices that are >>> >>>> 0 in the input will be excluded >>> (pruned) from the >>> >>>> smoothing mask. >>> >>>> >>> >>>> The mri_glmfit command is not right. >>> That command looks >>> >>>> like it is for analyzing each group >>> separately and >>> >>>> independently. If that is what you want >>> to do, then you >>> >>>> don't need to go through all the extra >>> stuff of >>> >>>> creating zero files, etc. I had assumed >>> that you wanted >>> >>>> to do some kind of comparisonbetween
>>> groups. If so, >>> >>>> then you would use a single filewith
>>> all your data in >>> >>>> it (probably what you were using >>> before), and your fsgd >>> >>>> file would have both groups. >>> >>>> >>> >>>> 1) will my fsgd file contain both groups? >>> >>>> yes, see above >>> >>>> 2) If the answer from question is yes, >>> i should have 2 >>> >>>> contrasts (pvr1.mtx for group1 and >>> pvr2.mtx for >>> >>>> group2). yes/no? >>> >>>> Again, if all you want to do is to test >>> the pvr for >>> >>>> each group separately, then youdon't
>>> need to go >>> >>>> through the processes of creating zero >>> files, etc. In >>> >>>> any event, if you want to test apvr,
>>> then you need a >>> >>>> contrast for it. >>> >>>> 3) below is a sample of my fsgdfile.
>>> are the >>> >>>> constrasts correct? >>> >>>> hard to say without resolving the >>> questions above. You >>> >>>> will need to have a value in the >>> contrast for each pvr. >>> >>>> >>> >>>> >>> >>>> >>> >>>> On 8/2/2019 3:56 PM, miracle ozzoude wrote: >>> >>>>> >>> >>>>> External Email - Use Caution >>> >>>>> >>> >>>>> Hello Doug, >>> >>>>> >>> >>>>> Thanks for answering. Based on your >>> explanation, i >>> >>>>> wrote out a series of command needed >>> to execute this. >>> >>>>> Please let me know if i made any >>> mistakes/correct. >>> >>>>> ##step1 concatenating the 10 amyloid >>> pet volumes files >>> >>>>> projected to surface using >>> mri_vol2surf for group1 >>> >>>>> mri_concat --f grp1.lhmgxctx --o >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune >>> >>>>> mri_concat --f grp2.rhmgxctx --o >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune >>> >>>>> >>> >>>>> ##step2 concatenating the 20 amyloid >>> pet volumes files >>> >>>>> projected to surface using >>> mri_vol2surf for group2 >>> >>>>> mri_concat --f grp2.lhmgxctx --o >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune >>> >>>>> mri_concat --f grp2.rhmgxctx --o >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune >>> >>>>> >>> >>>>> ##step3 smooth on the surface for each >>> hemisphere for >>> >>>>> group1 >>> >>>>> mri_surf2surf --hemi lh --s fsaverage >>> --sval >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm5
>>> >>>>> --cortex --tval >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> mri_surf2surf --hemi rh --s fsaverage >>> --sval >>> >>>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>> >>>>> --cortex --tval >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> >>> >>>>> ##step4 smooth on the surface for each >>> hemisphere for >>> >>>>> group2 >>> >>>>> mri_surf2surf --hemi lh --s fsaverage >>> --sval >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm5
>>> >>>>> --cortex --tval >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> mri_surf2surf --hemi rh --s fsaverage >>> --sval >>> >>>>> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>> >>>>> --cortex --tval >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> >>> >>>>> ##step5 create files of zeros for >>> group1 for each >>> >>>>> hemisphere >>> >>>>> fscalc >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> fscalc >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> >>> >>>>> ##step6 create files of zeros for >>> group2 for each >>> >>>>> hemisphere >>> >>>>> fscalc >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> fscalc >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> >>> >>>>> ##step7 create pvr files for group1 >>> for each hemisphere >>> >>>>> mri_concat >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz--o
>>> >>>>> lh.pvr_grp1_pet.nii.gz >>> >>>>> mri_concat >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz--o
>>> >>>>> rh.pvr_grp1_pet.nii.gz >>> >>>>> >>> >>>>> ##step8 create pvr files for group2 >>> for each hemisphere >>> >>>>> mri_concat >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o >>> >>>>> lh.pvr_grp2_pet.nii.gz >>> >>>>> mri_concat >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o >>> >>>>> rh.pvr_grp2_pet.nii.gz >>> >>>>> >>> >>>>> ###-----repeat steps 1-8 for cortical >>> thickness------- >>> >>>>> >>> >>>>> ###run glm-fit for group1 >>> >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr >>> >>>>> lh_pvr_grp1_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir lh.grp1.pet.thickness.glmdir >>> >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr >>> >>>>> rh_pvr_grp1_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir rh.grp1.pet.thickness.glmdir >>> >>>>> >>> >>>>> ###run glm-fit for group2 >>> >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>>> lh_pvr_grp2_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir lh.grp2.pet.thickness.glmdir >>> >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>>> rh_pvr_grp2_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir rh.grp2.pet.thickness.glmdir >>> >>>>> >>> >>>>> My questions. >>> >>>>> 1) will my fsgd file contain both groups? >>> >>>>> 2) If the answer from question is yes, >>> i should have 2 >>> >>>>> contrasts (pvr1.mtx for group1 and >>> pvr2.mtx for >>> >>>>> group2). yes/no? >>> >>>>> 3) below is a sample of my fsgd file. >>> are the >>> >>>>> constrasts correct? >>> >>>>> >>> >>>>> Thank you very much. >>> >>>>> Paul. >>> >>>>> The fsgd file lists: >>> >>>>> >>> ------------------------------------------------------------- >>> >>>>> GroupDescriptorFile 1 >>> >>>>> Title Relationship Amy-thick reg out >>> age and education >>> >>>>> Class g1 >>> >>>>> Class g2 >>> >>>>> Variable Age Education >>> >>>>> Input XX1 g1 60 16 >>> >>>>> Input YY1 g2 62 20 >>> >>>>> >>> ------------------------------------------------------------- >>> >>>>> matrix for group1: >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 >>> >>>>> is there a relationship between >>> amyloid-thickness in group1 regressing out age >>> >>>>> and education? >>> >>>>> matrix for group2: >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 >>> >>>>> is there a relationship between >>> amyloid-thickness in group2 regressing out age >>> >>>>> and education? >>> >>>>> >>> >>>>> On Thu, Aug 1, 2019 at 9:44 PM Greve, >>> Douglas N.,Ph.D. >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >>>>> >>> >>>>> Each PVR adds a single column to >>> the design >>> >>>>> matrix. In a two group design, >>> this can make it >>> >>>>> tricky to set up. Let's say you >>> have 10 of group1 >>> >>>>> and 20 of group2. You will need to >>> create two PVR >>> >>>>> files, each with 30=10+20 frames. >>> In the first >>> >>>>> one, the first 10 frames will be >>> cortical >>> >>>>> thickness (or amyloid sampled on >>> the surface) of >>> >>>>> group1; the next 20 frames will be >>> all zeros. For >>> >>>>> the 2nd PVR, the first 10 frames >>> will be 0s and >>> >>>>> the next 20 frames will be the >>> cortical thickness >>> >>>>> (or amyloid) for group2. I would >>> start by running >>> >>>>> mris_preproc for the two groups separate (so 2 >>> >>>>> files, one with 10 frames the >>> other 20 frames). >>> >>>>> Then create the file of zeros using >>> >>>>> fscalc group2.mgz mul 0 -o >>> group2.zeros.mgz >>> >>>>> Then >>> >>>>> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz >>> >>>>> Then create the contrast based on >>> the FSGD, but >>> >>>>> then add two more numbers, one for >>> PVR1 (which >>> >>>>> tests for the within group >>> correlation), and one >>> >>>>> for PVR2 >>> >>>>> >>> >>>>> >>> >>>>> On 8/1/2019 3:14 PM, miracle >>> ozzoude wrote: >>> >>>>>> >>> >>>>>> External Email - Use Caution >>> >>>>>> >>> >>>>>> Please, can anyone help me with this. >>> >>>>>> Thank you >>> >>>>>> >>> >>>>>> Paul >>> >>>>>> >>> >>>>>> ---------- Forwarded message --------- >>> >>>>>> From: *miracle ozzoude* >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM >>> >>>>>> Subject: multimodal analysis (pet andcortical
>>> >>>>>> thickness relationship) using --pvr >>> >>>>>> To: Douglas N Greve >>> >>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> Hello Experts, >>> >>>>>> >>> >>>>>> I am performing an analysis >>> looking at the >>> >>>>>> relationship between amyloid uptake and cortical >>> >>>>>> thickness using --pvr flag in mri_glmfit. I've 2 >>> >>>>>> groups and 2 variables (age and education). I >>> >>>>>> want to run a within group >>> analysis while >>> >>>>>> regressing out age and education (i.e. Within >>> >>>>>> group 1, is there a negative >>> relationship between >>> >>>>>> amyloid uptake and cortical thickness regressing >>> >>>>>> out the effects of age and >>> education). >>> >>>>>> >>> >>>>>> However, i'm not sure how my pvr contrasts will >>> >>>>>> look like. Below are my fsgd and >>> an attempt at >>> >>>>>> creating contrasts. Please, can you let me know >>> >>>>>> if my contrasts are correct based >>> on my questions. >>> >>>>>> >>> >>>>>> Thank you. >>> >>>>>> >>> >>>>>> Best, >>> >>>>>> Paul >>> >>>>>> >>> >>>>>> The fsgd file lists: >>> >>>>>> >>> ------------------------------------------------------------- >>> >>>>>> GroupDescriptorFile 1 >>> >>>>>> Title Relationship Amy-thick reg >>> out age and education >>> >>>>>> Class g1 >>> >>>>>> Class g2 >>> >>>>>> Variable Age Education >>> >>>>>> Input XX1 g1 60 16 >>> >>>>>> Input XX2 g1 58 14 >>> >>>>>> Input YY1 g2 62 20 >>> >>>>>> �� Input YY1 g2 62 20 >>> >>>>>> >>> ------------------------------------------------------------- >>> >>>>>> matrix for group1: >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 >>> >>>>>> is there a relationship between >>> amyloid-thickness in group1 regressing out age >>> >>>>>> and education? >>> >>>>>> matrix for group2: >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 >>> >>>>>> is there a relationship between >>> amyloid-thickness in group2 regressing out age >>> >>>>>> and education? >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> _______________________________________________ >>> >>>>>> Freesurfer mailing list >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> >>>>>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>>> >>> >>>>>
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14 Aug
14 Aug
11:16 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
Hey Doug,
If i want to do ROI surface base PET analysis using the method on the PETsurfer website. Please, how do i go about doing it? I know there series of commands i will need to run before project it to the surface using mri_vol2surf. thanks a lot best, Paul
On Tue, Aug 13, 2019 at 11:00 AM miracle ozzoude miracooloz@gmail.com wrote:
Awesome. thanks a lot for your help. I appreciate it.
Best, Paul
On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
You can use mri_surfcluster. That actually has an --fdr flag, so you should not need to run mri_fdr. When you use --fdr, you do not use --thmin. Use --sum to get the summary file
On 8/13/19 10:50 AM, miracle ozzoude wrote:
External Email - Use CautionThanks a lot doug. I want to use mri_fdr instead of mri_glmfit-sim. How do i get a summary of clusters like mri_glmfit-sim? I searched through the forum and based on previous responses, The advice was to do mri_fdr and then use mri_surfcluster without the fdr option to obtain the summary of cluster. Is this correct? Paul
On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
I don't know that there is much you can do. The PVR is very computationally intensive, and it does not surprise me that it is taking a long time. I don't think you need to do 10k permutations. I would start with 1k. In the output, you will get a confidence interval for the corrected p-value. This will shrink with the number of permutations, but if you're happy with it, no need to do more On 8/13/19 10:17 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Thanks Doug. My correction for multiple comparison using 10000 > permutation and abs has been running for 3days. This is strange > because i am using the --bg 10 and it usually takes 1hr to finish > without the --pvr. how do i solve this? > Below is my mri_glmfit and mri_glmfit-sim commands > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd dods --C $pvr1 > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf fsaverage lh > --cortex \ > --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save > > mri_glmfit-sim --glmdir ${wholebrain}/lh.pet.thickness.glmdir --perm > 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > You will have to click on the vertex you are interested in.The
> value will be -log10(pcorrected) where pcorrected is the corrected > p-value > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: >> >> External Email - Use Caution >> >> these regions (please see below) came out significant for the >> voxel-wise corrected map. I want to know their p-values. >> mri-glmfit-sim doesn't give summary file for voxel-wise corrected >> map only for cluster-wise map. >> image.png >> >> On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >> >> I'm not sure what you are looking for. The voxel-wise >> analysis is voxel-wise, so there is no summary file forit
>> >> On 8/12/2019 11:13 AM, miracle ozzoude wrote: >>> >>> External Email - Use Caution >>> >>> Thanks Doug. Another question, how do i find thep-values
>>> for voxel-wise map corrected for multiple comparisonsat a
>>> voxel (rather than cluster) level >>> (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. >>> Best, >>> Paul >>> >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: >>> >>> The 3 spaces is for left hemi, right hemi, and >>> subcortical, so, if you >>> are using all three then correct for all 3 >>> >>> On 8/7/19 9:26 AM, miracle ozzoude wrote: >>> > >>> > External Email - Use Caution >>> > >>> > Got it. Thanks a lot doug. If i have to correctfor
>>> multiple >>> > comparison in surface based pet analysis and >>> mutlimodal analysis (pet >>> > and thickness), should i use --3spaces? >>> > Thank you. >>> > >>> > best, >>> > Paul >>> > >>> > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> > >>> > I think there is still something not right.You
>>> should just have >>> > one mri_glmfit command for each hemisphere in >>> which the input is >>> > ?h.thickness.15.mgh, the fsgdfile is project.fsgd, >>> you then >>> > specify the pvrs for both groups (--pvr >>> ?h.pvr_grp1_pet.nii.gz >>> > --pvr ?h.pvr_grp2_pet.niigz) and then use that >>> first contrast. The >>> > second is the same as the first but with a >>> reversed sign, but it >>> > is not necessary since we always use unsigned >>> tests and show both >>> > signs (but you can still do it). >>> > >>> > On 8/5/2019 8:14 PM, miracle ozzoude wrote: >>> >> >>> >> External Email - Use Caution >>> >> >>> >> I think i got it now. Something like this: >>> >> >>> >> ## group1 comes first in my fsgd file.removing
>>> the effects of >>> >> age and education >>> >> ##amyloid-thickness. first pet pvr = 1 for group1 >>> and 0 for group 2. >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ >>> >> --pvr >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >> fsaverage lh --cortex --glmdir >>> lh.pet.thickness.glmdir >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ >>> >> --pvr >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage >>> >> lh --cortex --glmdir rh.pet.thickness.glmdir >>> >> >>> >> contrast = 0 0 0 0 0 0 1 -1 >>> >> >>> >> ##group 2 is second in my fsgd file. removing the >>> effects of age >>> >> and education >>> >> ##amyloid-thickness. first pet pvr = 0 for group1 >>> and 1 for group2 >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr2.mtx --pvr >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaveragelh
>>> --cortex --glmdir >>> >> rh.pet.thickness.glmdir >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd >>> project.fsgd dods --c >>> >> pvr2.mtx --pvr >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaveragelh
>>> --cortex --glmdir >>> >> rh.pet.thickness.glmdir >>> >> >>> >> contrast = 0 0 0 0 0 0 -1 1 >>> >> >>> >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas >>> N.,Ph.D. >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >> >>> >> It still looks like you are using a group >>> specific input >>> >> (--y). The input should be a simple file with >>> both groups >>> >> (same input as you would use without pvr) >>> >> >>> >> On 8/5/2019 4:39 PM, miracooloz wrote: >>> >>> >>> >>> External Email - Use Caution >>> >>> >>> >>> Thanks Doug. How about the mri_glmfit >>> commands? Since the >>> >>> contrasts are correct, I think the commands >>> should be right. >>> >>> >>> >>> Best, >>> >>> Paul. >>> >>> >>> >>> >>> >>> >>> >>> Sent from my Samsung Galaxy smartphone. >>> >>> >>> >>> -------- Original message -------- >>> >>> From: "Greve, Douglas N.,Ph.D." >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> >>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> >>> >>> Date: 2019-08-05 15:52 (GMT-05:00) >>> >>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> >>> >>> Subject: Re: [Freesurfer] Fwd:multimodal
>>> analysis (pet and >>> >>> cortical thickness relationship) using --pvr >>> >>> >>> >>> Yes, that contrast is correct. >>> >>> >>> >>> On 8/5/2019 3:11 PM, miracle ozzoude wrote: >>> >>>> >>> >>>> External Email - Use Caution >>> >>>> >>> >>>> Hello Doug, >>> >>>> >>> >>>> Thanks very much for your help. Your >>> assumption was right >>> >>>> in that i want to run a groupcomparison
>>> (i.e. test for a >>> >>>> difference in amyloid-thickness slopes >>> between the two >>> >>>> groups). However, I am having a hardtime
>>> creating the >>> >>>> correct mri_glmfit and contrasts inthis
>>> case. Based on >>> >>>> your advice and searching through the forum >>> >>>> >>> (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
>>> >>>> need 2 PVRs for each hemisphere in the >>> mri_glmfit command. >>> >>>> I gave it another shot below. Please let me >>> know if i am >>> >>>> correct. >>> >>>> >>> >>>> Thank you. >>> >>>> Paul. >>> >>>> >>> >>>> ## group1 comes first in my fsgd file. >>> removing the effects >>> >>>> of age and education >>> >>>> ##amyloid-thickness. first pet pvr = 1 for >>> group1 and 0 for >>> >>>> group 2. >>> >>>> mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr1.mtx --pvr >>> lh.pvr_grp1_pet.nii.gz \ >>> >>>> --pvr >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >>>> fsaverage lh --cortex --glmdir >>> lh.pet.thickness.glmdir >>> >>>> mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr1.mtx --pvr >>> rh.pvr_grp1_pet.nii.gz \ >>> >>>> --pvr >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf >>> >>>> fsaverage lh --cortex --glmdir >>> rh.pet.thickness.glmdir >>> >>>> >>> >>>> contrast = 0 0 0 0 0 0 1 -1 >>> >>>> >>> >>>> ##group 2 is second in my fsgd file. >>> removing the effects >>> >>>> of age and education >>> >>>> ##amyloid-thickness. first pet pvr = 0 for >>> group1 and 1 for >>> >>>> group2 >>> >>>> mri_glmfit --y >>> lh_pvr_grp2_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf >>> fsaverage lh --cortex >>> >>>> --glmdir rh.pet.thickness.glmdir >>> >>>> mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd >>> >>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf >>> fsaverage lh --cortex >>> >>>> --glmdir rh.pet.thickness.glmdir >>> >>>> >>> >>>> contrast = 0 0 0 0 0 0 -1 1 >>> >>>> >>> >>>> >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, >>> Douglas N.,Ph.D. >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >>>> >>> >>>> That mostly looks good. >>> >>>> >>> >>>> I would suggest is to change your >>> smoothing command to >>> >>>> something like >>> >>>> mris_fwhm --smooth-only --s fsaverage >>> --hemi lh --fwhm >>> >>>> 5 --cortex --prune --i >>> >>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>> The only difference will be thatany
>>> vertices that are >>> >>>> 0 in the input will be excluded >>> (pruned) from the >>> >>>> smoothing mask. >>> >>>> >>> >>>> The mri_glmfit command is notright.
>>> That command looks >>> >>>> like it is for analyzing each group >>> separately and >>> >>>> independently. If that is what you want >>> to do, then you >>> >>>> don't need to go through all the extra >>> stuff of >>> >>>> creating zero files, etc. I had assumed >>> that you wanted >>> >>>> to do some kind of comparisonbetween
>>> groups. If so, >>> >>>> then you would use a single filewith
>>> all your data in >>> >>>> it (probably what you were using >>> before), and your fsgd >>> >>>> file would have both groups. >>> >>>> >>> >>>> 1) will my fsgd file contain both groups? >>> >>>> yes, see above >>> >>>> 2) If the answer from question is yes, >>> i should have 2 >>> >>>> contrasts (pvr1.mtx for group1 and >>> pvr2.mtx for >>> >>>> group2). yes/no? >>> >>>> Again, if all you want to do is to test >>> the pvr for >>> >>>> each group separately, then youdon't
>>> need to go >>> >>>> through the processes of creating zero >>> files, etc. In >>> >>>> any event, if you want to test apvr,
>>> then you need a >>> >>>> contrast for it. >>> >>>> 3) below is a sample of my fsgdfile.
>>> are the >>> >>>> constrasts correct? >>> >>>> hard to say without resolving the >>> questions above. You >>> >>>> will need to have a value in the >>> contrast for each pvr. >>> >>>> >>> >>>> >>> >>>> >>> >>>> On 8/2/2019 3:56 PM, miracle ozzoude wrote: >>> >>>>> >>> >>>>> External Email - Use Caution >>> >>>>> >>> >>>>> Hello Doug, >>> >>>>> >>> >>>>> Thanks for answering. Based on your >>> explanation, i >>> >>>>> wrote out a series of command needed >>> to execute this. >>> >>>>> Please let me know if i made any >>> mistakes/correct. >>> >>>>> ##step1 concatenating the 10 amyloid >>> pet volumes files >>> >>>>> projected to surface using >>> mri_vol2surf for group1 >>> >>>>> mri_concat --f grp1.lhmgxctx --o >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz--prune
>>> >>>>> mri_concat --f grp2.rhmgxctx --o >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz--prune
>>> >>>>> >>> >>>>> ##step2 concatenating the 20 amyloid >>> pet volumes files >>> >>>>> projected to surface using >>> mri_vol2surf for group2 >>> >>>>> mri_concat --f grp2.lhmgxctx --o >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz--prune
>>> >>>>> mri_concat --f grp2.rhmgxctx --o >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz--prune
>>> >>>>> >>> >>>>> ##step3 smooth on the surface for each >>> hemisphere for >>> >>>>> group1 >>> >>>>> mri_surf2surf --hemi lh --s fsaverage >>> --sval >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz--fwhm 5
>>> >>>>> --cortex --tval >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> mri_surf2surf --hemi rh --s fsaverage >>> --sval >>> >>>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>> >>>>> --cortex --tval >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> >>> >>>>> ##step4 smooth on the surface for each >>> hemisphere for >>> >>>>> group2 >>> >>>>> mri_surf2surf --hemi lh --s fsaverage >>> --sval >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz--fwhm 5
>>> >>>>> --cortex --tval >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> mri_surf2surf --hemi rh --s fsaverage >>> --sval >>> >>>>> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 >>> >>>>> --cortex --tval >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> >>> >>>>> ##step5 create files of zeros for >>> group1 for each >>> >>>>> hemisphere >>> >>>>> fscalc >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> fscalc >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> >>> >>>>> ##step6 create files of zeros for >>> group2 for each >>> >>>>> hemisphere >>> >>>>> fscalc >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> fscalc >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> >>> >>>>> ##step7 create pvr files for group1 >>> for each hemisphere >>> >>>>> mri_concat >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz--o
>>> >>>>> lh.pvr_grp1_pet.nii.gz >>> >>>>> mri_concat >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz--o
>>> >>>>> rh.pvr_grp1_pet.nii.gz >>> >>>>> >>> >>>>> ##step8 create pvr files for group2 >>> for each hemisphere >>> >>>>> mri_concat >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o >>> >>>>> lh.pvr_grp2_pet.nii.gz >>> >>>>> mri_concat >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o >>> >>>>> rh.pvr_grp2_pet.nii.gz >>> >>>>> >>> >>>>> ###-----repeat steps 1-8 for cortical >>> thickness------- >>> >>>>> >>> >>>>> ###run glm-fit for group1 >>> >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr >>> >>>>> lh_pvr_grp1_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir lh.grp1.pet.thickness.glmdir >>> >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr >>> >>>>> rh_pvr_grp1_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir rh.grp1.pet.thickness.glmdir >>> >>>>> >>> >>>>> ###run glm-fit for group2 >>> >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>>> lh_pvr_grp2_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir lh.grp2.pet.thickness.glmdir >>> >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz >>> --fsgd >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr >>> >>>>> rh_pvr_grp2_thickness.mgh --surf fsaverage lh >>> --cortex >>> >>>>> --glmdir rh.grp2.pet.thickness.glmdir >>> >>>>> >>> >>>>> My questions. >>> >>>>> 1) will my fsgd file contain both groups? >>> >>>>> 2) If the answer from question is yes, >>> i should have 2 >>> >>>>> contrasts (pvr1.mtx for group1 and >>> pvr2.mtx for >>> >>>>> group2). yes/no? >>> >>>>> 3) below is a sample of my fsgd file. >>> are the >>> >>>>> constrasts correct? >>> >>>>> >>> >>>>> Thank you very much. >>> >>>>> Paul. >>> >>>>> The fsgd file lists: >>> >>>>> >>> ------------------------------------------------------------- >>> >>>>> GroupDescriptorFile 1 >>> >>>>> Title Relationship Amy-thick reg out >>> age and education >>> >>>>> Class g1 >>> >>>>> Class g2 >>> >>>>> Variable Age Education >>> >>>>> Input XX1 g1 60 16 >>> >>>>> Input YY1 g2 62 20 >>> >>>>> >>> ------------------------------------------------------------- >>> >>>>> matrix for group1: >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 >>> >>>>> is there a relationship between >>> amyloid-thickness in group1 regressing out age >>> >>>>> and education? >>> >>>>> matrix for group2: >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 >>> >>>>> is there a relationship between >>> amyloid-thickness in group2 regressing out age >>> >>>>> and education? >>> >>>>> >>> >>>>> On Thu, Aug 1, 2019 at 9:44 PM Greve, >>> Douglas N.,Ph.D. >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: >>> >>>>> >>> >>>>> Each PVR adds a single column to >>> the design >>> >>>>> matrix. In a two group design, >>> this can make it >>> >>>>> tricky to set up. Let's say you >>> have 10 of group1 >>> >>>>> and 20 of group2. You will need to >>> create two PVR >>> >>>>> files, each with 30=10+20 frames. >>> In the first >>> >>>>> one, the first 10 frames will be >>> cortical >>> >>>>> thickness (or amyloid sampled on >>> the surface) of >>> >>>>> group1; the next 20 frames will be >>> all zeros. For >>> >>>>> the 2nd PVR, the first 10 frames >>> will be 0s and >>> >>>>> the next 20 frames will be the >>> cortical thickness >>> >>>>> (or amyloid) for group2. I would >>> start by running >>> >>>>> mris_preproc for the two groups separate (so2
>>> >>>>> files, one with 10 frames the >>> other 20 frames). >>> >>>>> Then create the file of zeros using >>> >>>>> fscalc group2.mgz mul 0 -o >>> group2.zeros.mgz >>> >>>>> Then >>> >>>>> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz >>> >>>>> Then create the contrast based on >>> the FSGD, but >>> >>>>> then add two more numbers, one for >>> PVR1 (which >>> >>>>> tests for the within group >>> correlation), and one >>> >>>>> for PVR2 >>> >>>>> >>> >>>>> >>> >>>>> On 8/1/2019 3:14 PM, miracle >>> ozzoude wrote: >>> >>>>>> >>> >>>>>> External Email - Use Caution >>> >>>>>> >>> >>>>>> Please, can anyone help me with this. >>> >>>>>> Thank you >>> >>>>>> >>> >>>>>> Paul >>> >>>>>> >>> >>>>>> ---------- Forwarded message --------- >>> >>>>>> From: *miracle ozzoude* >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM >>> >>>>>> Subject: multimodal analysis (pet andcortical
>>> >>>>>> thickness relationship) using --pvr >>> >>>>>> To: Douglas N Greve >>> >>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> Hello Experts, >>> >>>>>> >>> >>>>>> I am performing an analysis >>> looking at the >>> >>>>>> relationship between amyloid uptake and cortical >>> >>>>>> thickness using --pvr flag in mri_glmfit. I've 2 >>> >>>>>> groups and 2 variables (age and education).I
>>> >>>>>> want to run a within group >>> analysis while >>> >>>>>> regressing out age and education (i.e.Within
>>> >>>>>> group 1, is there a negative >>> relationship between >>> >>>>>> amyloid uptake and cortical thickness regressing >>> >>>>>> out the effects of age and >>> education). >>> >>>>>> >>> >>>>>> However, i'm not sure how my pvr contrasts will >>> >>>>>> look like. Below are my fsgd and >>> an attempt at >>> >>>>>> creating contrasts. Please, can you let me know >>> >>>>>> if my contrasts are correct based >>> on my questions. >>> >>>>>> >>> >>>>>> Thank you. >>> >>>>>> >>> >>>>>> Best, >>> >>>>>> Paul >>> >>>>>> >>> >>>>>> The fsgd file lists: >>> >>>>>> >>> ------------------------------------------------------------- >>> >>>>>> GroupDescriptorFile 1 >>> >>>>>> Title Relationship Amy-thick reg >>> out age and education >>> >>>>>> Class g1 >>> >>>>>> Class g2 >>> >>>>>> Variable Age Education >>> >>>>>> Input XX1 g1 60 16 >>> >>>>>> Input XX2 g1 58 14 >>> >>>>>> Input YY1 g2 62 20 >>> >>>>>> �� Input YY1 g2 62 20 >>> >>>>>> >>> ------------------------------------------------------------- >>> >>>>>> matrix for group1: >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 >>> >>>>>> is there a relationship between >>> amyloid-thickness in group1 regressing out age >>> >>>>>> and education? >>> >>>>>> matrix for group2: >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 >>> >>>>>> is there a relationship between >>> amyloid-thickness in group2 regressing out age >>> >>>>>> and education? >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> _______________________________________________ >>> >>>>>> Freesurfer mailing list >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> >>>>>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>>> >>> >>>>>
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11:58 a.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
Do you mean using different ROIs than in the aparc? If you want to use the aparc, then that is done in the standard processing.
On 8/14/19 11:16 AM, miracle ozzoude wrote:
External Email - Use Caution
Hey Doug,
If i want to do ROI surface base PET analysis using the method on the PETsurfer website. Please, how do i go about doing it? I know there series of commands i will need to run before project it to the surface using mri_vol2surf. thanks a lot best, Paul
On Tue, Aug 13, 2019 at 11:00 AM miracle ozzoude <miracooloz@gmail.com mailto:miracooloz@gmail.com> wrote:
Awesome. thanks a lot for your help. I appreciate it. Best, Paul On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: You can use mri_surfcluster. That actually has an --fdr flag, so you should not need to run mri_fdr. When you use --fdr, you do not use --thmin. Use --sum to get the summary file On 8/13/19 10:50 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Thanks a lot doug. I want to use mri_fdr instead of mri_glmfit-sim. > How do i get a summary of clusters like mri_glmfit-sim? I searched > through the forum and based on previous responses, The advice was to > do mri_fdr and then use mri_surfcluster without the fdr option to > obtain the summary of cluster. Is this correct? > Paul > > On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I don't know that there is much you can do. The PVR is very > computationally intensive, and it does not surprise me that it is > taking > a long time. I don't think you need to do 10k permutations. I would > start with 1k. In the output, you will get a confidence interval > for the > corrected p-value. This will shrink with the number of > permutations, but > if you're happy with it, no need to do more > > On 8/13/19 10:17 AM, miracle ozzoude wrote: > > > > External Email - Use Caution > > > > Thanks Doug. My correction for multiple comparison using 10000 > > permutation and abs has been running for 3days. This is strange > > because i am using the --bg 10 and it usually takes 1hr to finish > > without the --pvr. how do i solve this? > > Below is my mri_glmfit and mri_glmfit-sim commands > > > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd dods --C $pvr1 > > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > > --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf > fsaverage lh > > --cortex \ > > --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save > > > > mri_glmfit-sim --glmdir ${wholebrain}/lh.pet.thickness.glmdir > --perm > > 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite > > > > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > You will have to click on the vertex you are interested in. The > > value will be -log10(pcorrected) where pcorrected is the > corrected > > p-value > > > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: > >> > >> External Email - Use Caution > >> > >> these regions (please see below) came out significant for the > >> voxel-wise corrected map. I want to know their p-values. > >> mri-glmfit-sim doesn't give summary file for voxel-wise > corrected > >> map only for cluster-wise map. > >> image.png > >> > >> On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. > >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > >> > >> I'm not sure what you are looking for. The voxel-wise > >> analysis is voxel-wise, so there is no summary file for it > >> > >> On 8/12/2019 11:13 AM, miracle ozzoude wrote: > >>> > >>> External Email - Use Caution > >>> > >>> Thanks Doug. Another question, how do i find the p-values > >>> for voxel-wise map corrected for multiple comparisons at a > >>> voxel (rather than cluster) level > >>> (perm.th40.abs.sig.voxel.mgh). There is no summary > file for it. > >>> Best, > >>> Paul > >>> > >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: > >>> > >>> The 3 spaces is for left hemi, right hemi, and > >>> subcortical, so, if you > >>> are using all three then correct for all 3 > >>> > >>> On 8/7/19 9:26 AM, miracle ozzoude wrote: > >>> > > >>> > External Email - Use Caution > >>> > > >>> > Got it. Thanks a lot doug. If i have to correct for > >>> multiple > >>> > comparison in surface based pet analysis and > >>> mutlimodal analysis (pet > >>> > and thickness), should i use --3spaces? > >>> > Thank you. > >>> > > >>> > best, > >>> > Paul > >>> > > >>> > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas > N.,Ph.D. > >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > >>> > > >>> > I think there is still something not right. You > >>> should just have > >>> > one mri_glmfit command for each hemisphere in > >>> which the input is > >>> > ?h.thickness.15.mgh, the fsgdfile is > project.fsgd, > >>> you then > >>> > specify the pvrs for both groups (--pvr > >>> ?h.pvr_grp1_pet.nii.gz > >>> > --pvr ?h.pvr_grp2_pet.niigz) and then use that > >>> first contrast. The > >>> > second is the same as the first but with a > >>> reversed sign, but it > >>> > is not necessary since we always use unsigned > >>> tests and show both > >>> > signs (but you can still do it). > >>> > > >>> > On 8/5/2019 8:14 PM, miracle ozzoude wrote: > >>> >> > >>> >> External Email - Use Caution > >>> >> > >>> >> I think i got it now. Something like this: > >>> >> > >>> >> ## group1 comes first in my fsgd file. removing > >>> the effects of > >>> >> age and education > >>> >> ##amyloid-thickness. first pet pvr = 1 for > group1 > >>> and 0 for group 2. > >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd > >>> project.fsgd dods --c > >>> >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ > >>> >> --pvr > >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >>> >> fsaverage lh --cortex --glmdir > >>> lh.pet.thickness.glmdir > >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd > >>> project.fsgd dods --c > >>> >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ > >>> >> --pvr > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage > >>> >> lh --cortex --glmdir rh.pet.thickness.glmdir > >>> >> > >>> >> contrast = 0 0 0 0 0 0 1 -1 > >>> >> > >>> >> ##group 2 is second in my fsgd file. > removing the > >>> effects of age > >>> >> and education > >>> >> ##amyloid-thickness. first pet pvr = 0 for > group1 > >>> and 1 for group2 > >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd > >>> project.fsgd dods --c > >>> >> pvr2.mtx --pvr > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>> >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh > >>> --cortex --glmdir > >>> >> rh.pet.thickness.glmdir > >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd > >>> project.fsgd dods --c > >>> >> pvr2.mtx --pvr > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>> >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh > >>> --cortex --glmdir > >>> >> rh.pet.thickness.glmdir > >>> >> > >>> >> contrast = 0 0 0 0 0 0 -1 1 > >>> >> > >>> >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas > >>> N.,Ph.D. > >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > >>> >> > >>> >> It still looks like you are using a group > >>> specific input > >>> >> (--y). The input should be a simple > file with > >>> both groups > >>> >> (same input as you would use without pvr) > >>> >> > >>> >> On 8/5/2019 4:39 PM, miracooloz wrote: > >>> >>> > >>> >>> External Email - Use Caution > >>> >>> > >>> >>> Thanks Doug. How about the mri_glmfit > >>> commands? Since the > >>> >>> contrasts are correct, I think the > commands > >>> should be right. > >>> >>> > >>> >>> Best, > >>> >>> Paul. > >>> >>> > >>> >>> > >>> >>> > >>> >>> Sent from my Samsung Galaxy smartphone. > >>> >>> > >>> >>> -------- Original message -------- > >>> >>> From: "Greve, Douglas N.,Ph.D." > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > >>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > >>> >>> Date: 2019-08-05 15:52 (GMT-05:00) > >>> >>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > >>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>> Subject: Re: [Freesurfer] Fwd: multimodal > >>> analysis (pet and > >>> >>> cortical thickness relationship) using > --pvr > >>> >>> > >>> >>> Yes, that contrast is correct. > >>> >>> > >>> >>> On 8/5/2019 3:11 PM, miracle ozzoude > wrote: > >>> >>>> > >>> >>>> External Email - Use Caution > >>> >>>> > >>> >>>> Hello Doug, > >>> >>>> > >>> >>>> Thanks very much for your help. Your > >>> assumption was right > >>> >>>> in that i want to run a group comparison > >>> (i.e. test for a > >>> >>>> difference in amyloid-thickness slopes > >>> between the two > >>> >>>> groups). However, I am having a hard time > >>> creating the > >>> >>>> correct mri_glmfit and contrasts in this > >>> case. Based on > >>> >>>> your advice and searching through the > forum > >>> >>>> > >>> > (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i > >>> >>>> need 2 PVRs for each hemisphere in the > >>> mri_glmfit command. > >>> >>>> I gave it another shot below. Please > let me > >>> know if i am > >>> >>>> correct. > >>> >>>> > >>> >>>> Thank you. > >>> >>>> Paul. > >>> >>>> > >>> >>>> ## group1 comes first in my fsgd file. > >>> removing the effects > >>> >>>> of age and education > >>> >>>> ##amyloid-thickness. first pet pvr = 1 for > >>> group1 and 0 for > >>> >>>> group 2. > >>> >>>> mri_glmfit --y > lh_pvr_grp1_thickness.mgh --fsgd > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > >>> lh.pvr_grp1_pet.nii.gz \ > >>> >>>> --pvr > >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >>> >>>> fsaverage lh --cortex --glmdir > >>> lh.pet.thickness.glmdir > >>> >>>> mri_glmfit --y > rh_pvr_grp1_thickness.mgh --fsgd > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > >>> rh.pvr_grp1_pet.nii.gz \ > >>> >>>> --pvr > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >>> >>>> fsaverage lh --cortex --glmdir > >>> rh.pet.thickness.glmdir > >>> >>>> > >>> >>>> contrast = 0 0 0 0 0 0 1 -1 > >>> >>>> > >>> >>>> ##group 2 is second in my fsgd file. > >>> removing the effects > >>> >>>> of age and education > >>> >>>> ##amyloid-thickness. first pet pvr = 0 for > >>> group1 and 1 for > >>> >>>> group2 > >>> >>>> mri_glmfit --y > >>> lh_pvr_grp2_thickness.mgh --fsgd > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf > >>> fsaverage lh --cortex > >>> >>>> --glmdir rh.pet.thickness.glmdir > >>> >>>> mri_glmfit --y > rh_pvr_grp2_thickness.mgh --fsgd > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > >>> >>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf > >>> fsaverage lh --cortex > >>> >>>> --glmdir rh.pet.thickness.glmdir > >>> >>>> > >>> >>>> contrast = 0 0 0 0 0 0 -1 1 > >>> >>>> > >>> >>>> > >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, > >>> Douglas N.,Ph.D. > >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > >>> >>>> > >>> >>>> That mostly looks good. > >>> >>>> > >>> >>>> I would suggest is to change your > >>> smoothing command to > >>> >>>> something like > >>> >>>> mris_fwhm --smooth-only --s fsaverage > >>> --hemi lh --fwhm > >>> >>>> 5 --cortex --prune --i > >>> >>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > >>> >>>> The only difference will be that any > >>> vertices that are > >>> >>>> 0 in the input will be excluded > >>> (pruned) from the > >>> >>>> smoothing mask. > >>> >>>> > >>> >>>> The mri_glmfit command is not right. > >>> That command looks > >>> >>>> like it is for analyzing each group > >>> separately and > >>> >>>> independently. If that is what you want > >>> to do, then you > >>> >>>> don't need to go through all the > extra > >>> stuff of > >>> >>>> creating zero files, etc. I had > assumed > >>> that you wanted > >>> >>>> to do some kind of comparison between > >>> groups. If so, > >>> >>>> then you would use a single file with > >>> all your data in > >>> >>>> it (probably what you were using > >>> before), and your fsgd > >>> >>>> file would have both groups. > >>> >>>> > >>> >>>> 1) will my fsgd file contain both > groups? > >>> >>>> yes, see above > >>> >>>> 2) If the answer from question is > yes, > >>> i should have 2 > >>> >>>> contrasts (pvr1.mtx for group1 and > >>> pvr2.mtx for > >>> >>>> group2). yes/no? > >>> >>>> Again, if all you want to do is > to test > >>> the pvr for > >>> >>>> each group separately, then you don't > >>> need to go > >>> >>>> through the processes of creating > zero > >>> files, etc. In > >>> >>>> any event, if you want to test a pvr, > >>> then you need a > >>> >>>> contrast for it. > >>> >>>> 3) below is a sample of my fsgd file. > >>> are the > >>> >>>> constrasts correct? > >>> >>>> hard to say without resolving the > >>> questions above. You > >>> >>>> will need to have a value in the > >>> contrast for each pvr. > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> On 8/2/2019 3:56 PM, miracle > ozzoude wrote: > >>> >>>>> > >>> >>>>> External Email - Use Caution > >>> >>>>> > >>> >>>>> Hello Doug, > >>> >>>>> > >>> >>>>> Thanks for answering. Based on your > >>> explanation, i > >>> >>>>> wrote out a series of command needed > >>> to execute this. > >>> >>>>> Please let me know if i made any > >>> mistakes/correct. > >>> >>>>> ##step1 concatenating the 10 amyloid > >>> pet volumes files > >>> >>>>> projected to surface using > >>> mri_vol2surf for group1 > >>> >>>>> mri_concat --f grp1.lhmgxctx --o > >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > >>> >>>>> > >>> >>>>> ##step2 concatenating the 20 amyloid > >>> pet volumes files > >>> >>>>> projected to surface using > >>> mri_vol2surf for group2 > >>> >>>>> mri_concat --f grp2.lhmgxctx --o > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > >>> >>>>> > >>> >>>>> ##step3 smooth on the surface for each > >>> hemisphere for > >>> >>>>> group1 > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > >>> --sval > >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > >>> >>>>> --cortex --tval > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > >>> --sval > >>> >>>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > --fwhm 5 > >>> >>>>> --cortex --tval > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> > >>> >>>>> ##step4 smooth on the surface for each > >>> hemisphere for > >>> >>>>> group2 > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > >>> --sval > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > >>> >>>>> --cortex --tval > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > >>> --sval > >>> >>>>> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz > --fwhm 5 > >>> >>>>> --cortex --tval > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> > >>> >>>>> ##step5 create files of zeros for > >>> group1 for each > >>> >>>>> hemisphere > >>> >>>>> fscalc > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> fscalc > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> > >>> >>>>> ##step6 create files of zeros for > >>> group2 for each > >>> >>>>> hemisphere > >>> >>>>> fscalc > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> fscalc > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> > >>> >>>>> ##step7 create pvr files for group1 > >>> for each hemisphere > >>> >>>>> mri_concat > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > >>> >>>>> lh.pvr_grp1_pet.nii.gz > >>> >>>>> mri_concat > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > >>> >>>>> rh.pvr_grp1_pet.nii.gz > >>> >>>>> > >>> >>>>> ##step8 create pvr files for group2 > >>> for each hemisphere > >>> >>>>> mri_concat > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > >>> >>>>> lh.pvr_grp2_pet.nii.gz > >>> >>>>> mri_concat > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > >>> >>>>> rh.pvr_grp2_pet.nii.gz > >>> >>>>> > >>> >>>>> ###-----repeat steps 1-8 for cortical > >>> thickness------- > >>> >>>>> > >>> >>>>> ###run glm-fit for group1 > >>> >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz > >>> --fsgd > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > >>> >>>>> lh_pvr_grp1_thickness.mgh --surf fsaverage lh > >>> --cortex > >>> >>>>> --glmdir lh.grp1.pet.thickness.glmdir > >>> >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz > >>> --fsgd > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > >>> >>>>> rh_pvr_grp1_thickness.mgh --surf fsaverage lh > >>> --cortex > >>> >>>>> --glmdir rh.grp1.pet.thickness.glmdir > >>> >>>>> > >>> >>>>> ###run glm-fit for group2 > >>> >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz > >>> --fsgd > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > >>> >>>>> lh_pvr_grp2_thickness.mgh --surf fsaverage lh > >>> --cortex > >>> >>>>> --glmdir lh.grp2.pet.thickness.glmdir > >>> >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz > >>> --fsgd > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > >>> >>>>> rh_pvr_grp2_thickness.mgh --surf fsaverage lh > >>> --cortex > >>> >>>>> --glmdir rh.grp2.pet.thickness.glmdir > >>> >>>>> > >>> >>>>> My questions. > >>> >>>>> 1) will my fsgd file contain > both groups? > >>> >>>>> 2) If the answer from question > is yes, > >>> i should have 2 > >>> >>>>> contrasts (pvr1.mtx for group1 and > >>> pvr2.mtx for > >>> >>>>> group2). yes/no? > >>> >>>>> 3) below is a sample of my fsgd > file. > >>> are the > >>> >>>>> constrasts correct? > >>> >>>>> > >>> >>>>> Thank you very much. > >>> >>>>> Paul. > >>> >>>>> The fsgd file lists: > >>> >>>>> > >>> ------------------------------------------------------------- > >>> >>>>> GroupDescriptorFile 1 > >>> >>>>> Title Relationship Amy-thick reg out > >>> age and education > >>> >>>>> Class g1 > >>> >>>>> Class g2 > >>> >>>>> Variable Age Education > >>> >>>>> Input XX1 g1 60 16 > >>> >>>>> Input YY1 g2 62 20 > >>> >>>>> > >>> ------------------------------------------------------------- > >>> >>>>> matrix for group1: > >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 > >>> >>>>> is there a relationship between > >>> amyloid-thickness in group1 regressing out age > >>> >>>>> and education? > >>> >>>>> matrix for group2: > >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 > >>> >>>>> is there a relationship between > >>> amyloid-thickness in group2 regressing out age > >>> >>>>> and education? > >>> >>>>> > >>> >>>>> On Thu, Aug 1, 2019 at 9:44 PM > Greve, > >>> Douglas N.,Ph.D. > >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > >>> >>>>> > >>> >>>>> Each PVR adds a single column to > >>> the design > >>> >>>>> matrix. In a two group design, > >>> this can make it > >>> >>>>> tricky to set up. Let's say you > >>> have 10 of group1 > >>> >>>>> and 20 of group2. You will need to > >>> create two PVR > >>> >>>>> files, each with 30=10+20 frames. > >>> In the first > >>> >>>>> one, the first 10 frames will be > >>> cortical > >>> >>>>> thickness (or amyloid sampled on > >>> the surface) of > >>> >>>>> group1; the next 20 frames will be > >>> all zeros. For > >>> >>>>> the 2nd PVR, the first 10 frames > >>> will be 0s and > >>> >>>>> the next 20 frames will be the > >>> cortical thickness > >>> >>>>> (or amyloid) for group2. I would > >>> start by running > >>> >>>>> mris_preproc for the two groups separate (so 2 > >>> >>>>> files, one with 10 frames the > >>> other 20 frames). > >>> >>>>> Then create the file of zeros using > >>> >>>>> fscalc group2.mgz mul 0 -o > >>> group2.zeros.mgz > >>> >>>>> Then > >>> >>>>> mri_concat group1.mgz group2.zeros.mgz --o > pvr1.mgz > >>> >>>>> Then create the contrast based on > >>> the FSGD, but > >>> >>>>> then add two more numbers, one for > >>> PVR1 (which > >>> >>>>> tests for the within group > >>> correlation), and one > >>> >>>>> for PVR2 > >>> >>>>> > >>> >>>>> > >>> >>>>> On 8/1/2019 3:14 PM, miracle > >>> ozzoude wrote: > >>> >>>>>> > >>> >>>>>> External Email - Use Caution > >>> >>>>>> > >>> >>>>>> Please, can anyone help me with this. > >>> >>>>>> Thank you > >>> >>>>>> > >>> >>>>>> Paul > >>> >>>>>> > >>> >>>>>> ---------- Forwarded message --------- > >>> >>>>>> From: *miracle ozzoude* > >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> > >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM > >>> >>>>>> Subject: multimodal analysis (pet and cortical > >>> >>>>>> thickness relationship) using --pvr > >>> >>>>>> To: Douglas N Greve > >>> >>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > >>> >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > >>> >>>>>> > >>> >>>>>> > >>> >>>>>> Hello Experts, > >>> >>>>>> > >>> >>>>>> I am performing an analysis > >>> looking at the > >>> >>>>>> relationship between amyloid uptake and > cortical > >>> >>>>>> thickness using --pvr flag in mri_glmfit. > I've 2 > >>> >>>>>> groups and 2 variables (age and education). I > >>> >>>>>> want to run a within group > >>> analysis while > >>> >>>>>> regressing out age and education (i.e. Within > >>> >>>>>> group 1, is there a negative > >>> relationship between > >>> >>>>>> amyloid uptake and cortical thickness > regressing > >>> >>>>>> out the effects of age and > >>> education). > >>> >>>>>> > >>> >>>>>> However, i'm not sure how my pvr contrasts > will > >>> >>>>>> look like. Below are my fsgd and > >>> an attempt at > >>> >>>>>> creating contrasts. Please, can you let me > know > >>> >>>>>> if my contrasts are correct based > >>> on my questions. > >>> >>>>>> > >>> >>>>>> Thank you. > >>> >>>>>> > >>> >>>>>> Best, > >>> >>>>>> Paul > >>> >>>>>> > >>> >>>>>> The fsgd file lists: > >>> >>>>>> > >>> ------------------------------------------------------------- > >>> >>>>>> GroupDescriptorFile 1 > >>> >>>>>> Title Relationship Amy-thick reg > >>> out age and education > >>> >>>>>> Class g1 > >>> >>>>>> Class g2 > >>> >>>>>> Variable Age Education > >>> >>>>>> Input XX1 g1 60 16 > >>> >>>>>> Input XX2 g1 58 14 > >>> >>>>>> Input YY1 g2 62 20 > >>> >>>>>> �� Input YY1 g2 62 20 > >>> >>>>>> > >>> ------------------------------------------------------------- > >>> >>>>>> matrix for group1: > >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 > >>> >>>>>> is there a relationship between > >>> amyloid-thickness in group1 regressing out age > >>> >>>>>> and education? > >>> >>>>>> matrix for group2: > >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 > >>> >>>>>> is there a relationship between > >>> amyloid-thickness in group2 regressing out age > >>> >>>>>> and education? > >>> >>>>>> > >>> >>>>>> > >>> >>>>>> > >>> >>>>>> > >>> >>>>>> > _______________________________________________ > >>> >>>>>> Freesurfer mailing list > >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >>>>> > >>> >>>>> _______________________________________________ > >>> >>>>> Freesurfer mailing list > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >>>>> > >>> >>>>> > >>> >>>>> _______________________________________________ > >>> >>>>> Freesurfer mailing list > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >>>> > >>> >>>> _______________________________________________ > >>> >>>> Freesurfer mailing list > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >>>> > >>> >>>> > >>> >>>> _______________________________________________ > >>> >>>> Freesurfer mailing list > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >>> > >>> >>> > >>> >>> _______________________________________________ > >>> >>> Freesurfer mailing list > >>> >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >> > >>> >> _______________________________________________ > >>> >> Freesurfer mailing list > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >> > >>> >> > >>> >> _______________________________________________ > >>> >> Freesurfer mailing list > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu 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12:59 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
I want to use the aparc ROI. something similar to doing ROI surface base cortical thickness analysis where i used mri_annotation2label to extract the regions and mri_mergelabels to merge them and run analysis on them.
On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Do you mean using different ROIs than in the aparc? If you want to use the aparc, then that is done in the standard processing.
On 8/14/19 11:16 AM, miracle ozzoude wrote:
External Email - Use CautionHey Doug,
If i want to do ROI surface base PET analysis using the method on the PETsurfer website. Please, how do i go about doing it? I know there series of commands i will need to run before project it to the surface using mri_vol2surf. thanks a lot best, Paul
On Tue, Aug 13, 2019 at 11:00 AM miracle ozzoude <miracooloz@gmail.com mailto:miracooloz@gmail.com> wrote:
Awesome. thanks a lot for your help. I appreciate it. Best, Paul On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: You can use mri_surfcluster. That actually has an --fdr flag, so you should not need to run mri_fdr. When you use --fdr, you do not use --thmin. Use --sum to get the summary file On 8/13/19 10:50 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Thanks a lot doug. I want to use mri_fdr instead of mri_glmfit-sim. > How do i get a summary of clusters like mri_glmfit-sim? I searched > through the forum and based on previous responses, The advice was to > do mri_fdr and then use mri_surfcluster without the fdr option to > obtain the summary of cluster. Is this correct? > Paul > > On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I don't know that there is much you can do. The PVR is very > computationally intensive, and it does not surprise me that it is > taking > a long time. I don't think you need to do 10k permutations. I would > start with 1k. In the output, you will get a confidence interval > for the > corrected p-value. This will shrink with the number of > permutations, but > if you're happy with it, no need to do more > > On 8/13/19 10:17 AM, miracle ozzoude wrote: > > > > External Email - Use Caution > > > > Thanks Doug. My correction for multiple comparison using 10000 > > permutation and abs has been running for 3days. This is strange > > because i am using the --bg 10 and it usually takes 1hr to finish > > without the --pvr. how do i solve this? > > Below is my mri_glmfit and mri_glmfit-sim commands > > > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd dods --C $pvr1 > > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > > --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf > fsaverage lh > > --cortex \ > > --glmdir ${wholebrain}/lh.pet.thickness.glmdir--eres-save
> > > > mri_glmfit-sim --glmdir ${wholebrain}/lh.pet.thickness.glmdir > --perm > > 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite > > > > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > You will have to click on the vertex you are interested in. The > > value will be -log10(pcorrected) where pcorrected is the > corrected > > p-value > > > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: > >> > >> External Email - Use Caution > >> > >> these regions (please see below) came out significant for the > >> voxel-wise corrected map. I want to know their p-values. > >> mri-glmfit-sim doesn't give summary file for voxel-wise > corrected > >> map only for cluster-wise map. > >> image.png > >> > >> On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. > >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > >> > >> I'm not sure what you are looking for. The voxel-wise > >> analysis is voxel-wise, so there is no summary file for it > >> > >> On 8/12/2019 11:13 AM, miracle ozzoude wrote: > >>> > >>> External Email - Use Caution > >>> > >>> Thanks Doug. Another question, how do i find the p-values > >>> for voxel-wise map corrected for multiple comparisons at a > >>> voxel (rather than cluster) level > >>> (perm.th40.abs.sig.voxel.mgh). There is no summary > file for it. > >>> Best, > >>> Paul > >>> > >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: > >>> > >>> The 3 spaces is for left hemi, right hemi, and > >>> subcortical, so, if you > >>> are using all three then correct for all 3 > >>> > >>> On 8/7/19 9:26 AM, miracle ozzoude wrote: > >>> > > >>> > External Email - Use Caution > >>> > > >>> > Got it. Thanks a lot doug. If i have to correct for > >>> multiple > >>> > comparison in surface based pet analysis and > >>> mutlimodal analysis (pet > >>> > and thickness), should i use --3spaces? > >>> > Thank you. > >>> > > >>> > best, > >>> > Paul > >>> > > >>> > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas > N.,Ph.D. > >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > >>> > > >>> > I think there is still something not right. You > >>> should just have > >>> > one mri_glmfit command for each hemisphere in > >>> which the input is > >>> > ?h.thickness.15.mgh, the fsgdfile is > project.fsgd, > >>> you then > >>> > specify the pvrs for both groups (--pvr > >>> ?h.pvr_grp1_pet.nii.gz > >>> > --pvr ?h.pvr_grp2_pet.niigz) and then use that > >>> first contrast. The > >>> > second is the same as the first but with a > >>> reversed sign, but it > >>> > is not necessary since we always use unsigned > >>> tests and show both > >>> > signs (but you can still do it). > >>> > > >>> > On 8/5/2019 8:14 PM, miracle ozzoude wrote: > >>> >> > >>> >> External Email - Use Caution > >>> >> > >>> >> I think i got it now. Something like this: > >>> >> > >>> >> ## group1 comes first in my fsgd file. removing > >>> the effects of > >>> >> age and education > >>> >> ##amyloid-thickness. first pet pvr = 1 for > group1 > >>> and 0 for group 2. > >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd > >>> project.fsgd dods --c > >>> >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ > >>> >> --pvr > >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >>> >> fsaverage lh --cortex --glmdir > >>> lh.pet.thickness.glmdir > >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd > >>> project.fsgd dods --c > >>> >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ > >>> >> --pvr > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage > >>> >> lh --cortex --glmdir rh.pet.thickness.glmdir > >>> >> > >>> >> contrast = 0 0 0 0 0 0 1 -1 > >>> >> > >>> >> ##group 2 is second in my fsgd file. > removing the > >>> effects of age > >>> >> and education > >>> >> ##amyloid-thickness. first pet pvr = 0 for > group1 > >>> and 1 for group2 > >>> >> mri_glmfit --y lh.thickness.15.mgh --fsgd > >>> project.fsgd dods --c > >>> >> pvr2.mtx --pvr > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>> >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh > >>> --cortex --glmdir > >>> >> rh.pet.thickness.glmdir > >>> >> mri_glmfit --y rh.thickness.15.mgh --fsgd > >>> project.fsgd dods --c > >>> >> pvr2.mtx --pvr > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>> >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh > >>> --cortex --glmdir > >>> >> rh.pet.thickness.glmdir > >>> >> > >>> >> contrast = 0 0 0 0 0 0 -1 1 > >>> >> > >>> >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas > >>> N.,Ph.D. > >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > >>> >> > >>> >> It still looks like you are using a group > >>> specific input > >>> >> (--y). The input should be a simple > file with > >>> both groups > >>> >> (same input as you would use without pvr) > >>> >> > >>> >> On 8/5/2019 4:39 PM, miracooloz wrote: > >>> >>> > >>> >>> External Email - Use Caution > >>> >>> > >>> >>> Thanks Doug. How about the mri_glmfit > >>> commands? Since the > >>> >>> contrasts are correct, I think the > commands > >>> should be right. > >>> >>> > >>> >>> Best, > >>> >>> Paul. > >>> >>> > >>> >>> > >>> >>> > >>> >>> Sent from my Samsung Galaxysmartphone.
> >>> >>> > >>> >>> -------- Original message -------- > >>> >>> From: "Greve, Douglas N.,Ph.D." > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > >>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > >>> >>> Date: 2019-08-05 15:52 (GMT-05:00) > >>> >>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > >>> >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>> Subject: Re: [Freesurfer] Fwd: multimodal > >>> analysis (pet and > >>> >>> cortical thickness relationship) using > --pvr > >>> >>> > >>> >>> Yes, that contrast is correct. > >>> >>> > >>> >>> On 8/5/2019 3:11 PM, miracle ozzoude > wrote: > >>> >>>> > >>> >>>> External Email - Use Caution > >>> >>>> > >>> >>>> Hello Doug, > >>> >>>> > >>> >>>> Thanks very much for your help. Your > >>> assumption was right > >>> >>>> in that i want to run a group comparison > >>> (i.e. test for a > >>> >>>> difference in amyloid-thicknessslopes
> >>> between the two > >>> >>>> groups). However, I am having a hard time > >>> creating the > >>> >>>> correct mri_glmfit and contrasts in this > >>> case. Based on > >>> >>>> your advice and searching through the > forum > >>> >>>> > >>> > (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
> >>> >>>> need 2 PVRs for each hemisphere inthe
> >>> mri_glmfit command. > >>> >>>> I gave it another shot below. Please > let me > >>> know if i am > >>> >>>> correct. > >>> >>>> > >>> >>>> Thank you. > >>> >>>> Paul. > >>> >>>> > >>> >>>> ## group1 comes first in my fsgdfile.
> >>> removing the effects > >>> >>>> of age and education > >>> >>>> ##amyloid-thickness. first pet pvr = 1 for > >>> group1 and 0 for > >>> >>>> group 2. > >>> >>>> mri_glmfit --y > lh_pvr_grp1_thickness.mgh --fsgd > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > >>> lh.pvr_grp1_pet.nii.gz \ > >>> >>>> --pvr > >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >>> >>>> fsaverage lh --cortex --glmdir > >>> lh.pet.thickness.glmdir > >>> >>>> mri_glmfit --y > rh_pvr_grp1_thickness.mgh --fsgd > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > >>> rh.pvr_grp1_pet.nii.gz \ > >>> >>>> --pvr > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >>> >>>> fsaverage lh --cortex --glmdir > >>> rh.pet.thickness.glmdir > >>> >>>> > >>> >>>> contrast = 0 0 0 0 0 0 1 -1 > >>> >>>> > >>> >>>> ##group 2 is second in my fsgd file. > >>> removing the effects > >>> >>>> of age and education > >>> >>>> ##amyloid-thickness. first pet pvr = 0 for > >>> group1 and 1 for > >>> >>>> group2 > >>> >>>> mri_glmfit --y > >>> lh_pvr_grp2_thickness.mgh --fsgd > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf > >>> fsaverage lh --cortex > >>> >>>> --glmdir rh.pet.thickness.glmdir > >>> >>>> mri_glmfit --y > rh_pvr_grp2_thickness.mgh --fsgd > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > >>> >>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf > >>> fsaverage lh --cortex > >>> >>>> --glmdir rh.pet.thickness.glmdir > >>> >>>> > >>> >>>> contrast = 0 0 0 0 0 0 -1 1 > >>> >>>> > >>> >>>> > >>> >>>> On Mon, Aug 5, 2019 at 12:26 PMGreve,
> >>> Douglas N.,Ph.D. > >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > >>> >>>> > >>> >>>> That mostly looks good. > >>> >>>> > >>> >>>> I would suggest is to change your > >>> smoothing command to > >>> >>>> something like > >>> >>>> mris_fwhm --smooth-only --s fsaverage > >>> --hemi lh --fwhm > >>> >>>> 5 --cortex --prune --i > >>> >>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > >>> >>>>allgrp1.lhmgxctx.fsaverage.sm05.nii.gz
> >>> >>>> The only difference will be that any > >>> vertices that are > >>> >>>> 0 in the input will be excluded > >>> (pruned) from the > >>> >>>> smoothing mask. > >>> >>>> > >>> >>>> The mri_glmfit command is not right. > >>> That command looks > >>> >>>> like it is for analyzing each group > >>> separately and > >>> >>>> independently. If that is what you want > >>> to do, then you > >>> >>>> don't need to go through all the > extra > >>> stuff of > >>> >>>> creating zero files, etc. I had > assumed > >>> that you wanted > >>> >>>> to do some kind of comparison between > >>> groups. If so, > >>> >>>> then you would use a single file with > >>> all your data in > >>> >>>> it (probably what you were using > >>> before), and your fsgd > >>> >>>> file would have both groups. > >>> >>>> > >>> >>>> 1) will my fsgd file contain both > groups? > >>> >>>> yes, see above > >>> >>>> 2) If the answer from question is > yes, > >>> i should have 2 > >>> >>>> contrasts (pvr1.mtx for group1 and > >>> pvr2.mtx for > >>> >>>> group2). yes/no? > >>> >>>> Again, if all you want to do is > to test > >>> the pvr for > >>> >>>> each group separately, then you don't > >>> need to go > >>> >>>> through the processes of creating > zero > >>> files, etc. In > >>> >>>> any event, if you want to test a pvr, > >>> then you need a > >>> >>>> contrast for it. > >>> >>>> 3) below is a sample of my fsgd file. > >>> are the > >>> >>>> constrasts correct? > >>> >>>> hard to say without resolving the > >>> questions above. You > >>> >>>> will need to have a value in the > >>> contrast for each pvr. > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> On 8/2/2019 3:56 PM, miracle > ozzoude wrote: > >>> >>>>> > >>> >>>>> External Email - Use Caution > >>> >>>>> > >>> >>>>> Hello Doug, > >>> >>>>> > >>> >>>>> Thanks for answering. Based on your > >>> explanation, i > >>> >>>>> wrote out a series of command needed > >>> to execute this. > >>> >>>>> Please let me know if i made any > >>> mistakes/correct. > >>> >>>>> ##step1 concatenating the 10 amyloid > >>> pet volumes files > >>> >>>>> projected to surface using > >>> mri_vol2surf for group1 > >>> >>>>> mri_concat --f grp1.lhmgxctx --o > >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > >>> >>>>> > >>> >>>>> ##step2 concatenating the 20 amyloid > >>> pet volumes files > >>> >>>>> projected to surface using > >>> mri_vol2surf for group2 > >>> >>>>> mri_concat --f grp2.lhmgxctx --o > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > >>> >>>>> > >>> >>>>> ##step3 smooth on the surface for each > >>> hemisphere for > >>> >>>>> group1 > >>> >>>>> mri_surf2surf --hemi lh --sfsaverage
> >>> --sval > >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > >>> >>>>> --cortex --tval > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> mri_surf2surf --hemi rh --sfsaverage
> >>> --sval > >>> >>>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > --fwhm 5 > >>> >>>>> --cortex --tval > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> > >>> >>>>> ##step4 smooth on the surface for each > >>> hemisphere for > >>> >>>>> group2 > >>> >>>>> mri_surf2surf --hemi lh --sfsaverage
> >>> --sval > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > >>> >>>>> --cortex --tval > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> mri_surf2surf --hemi rh --sfsaverage
> >>> --sval > >>> >>>>> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz > --fwhm 5 > >>> >>>>> --cortex --tval > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> > >>> >>>>> ##step5 create files of zeros for > >>> group1 for each > >>> >>>>> hemisphere > >>> >>>>> fscalc > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>> >>>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> fscalc > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>> >>>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> > >>> >>>>> ##step6 create files of zeros for > >>> group2 for each > >>> >>>>> hemisphere > >>> >>>>> fscalc > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> fscalc > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> > >>> >>>>> ##step7 create pvr files for group1 > >>> for each hemisphere > >>> >>>>> mri_concat > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > >>> >>>>> lh.pvr_grp1_pet.nii.gz > >>> >>>>> mri_concat > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > >>> >>>>> rh.pvr_grp1_pet.nii.gz > >>> >>>>> > >>> >>>>> ##step8 create pvr files for group2 > >>> for each hemisphere > >>> >>>>> mri_concat > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > >>> >>>>> lh.pvr_grp2_pet.nii.gz > >>> >>>>> mri_concat > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>> >>>>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > >>> >>>>> rh.pvr_grp2_pet.nii.gz > >>> >>>>> > >>> >>>>> ###-----repeat steps 1-8 for cortical > >>> thickness------- > >>> >>>>> > >>> >>>>> ###run glm-fit for group1 > >>> >>>>> mri_glmfit --ylh.pvr_grp1_pet.nii.gz
> >>> --fsgd > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > >>> >>>>> lh_pvr_grp1_thickness.mgh --surf fsaverage lh > >>> --cortex > >>> >>>>> --glmdirlh.grp1.pet.thickness.glmdir
> >>> >>>>> mri_glmfit --yrh.pvr_grp1_pet.nii.gz
> >>> --fsgd > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > >>> >>>>> rh_pvr_grp1_thickness.mgh --surf fsaverage lh > >>> --cortex > >>> >>>>> --glmdirrh.grp1.pet.thickness.glmdir
> >>> >>>>> > >>> >>>>> ###run glm-fit for group2 > >>> >>>>> mri_glmfit --ylh.pvr_grp2_pet.nii.gz
> >>> --fsgd > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > >>> >>>>> lh_pvr_grp2_thickness.mgh --surf fsaverage lh > >>> --cortex > >>> >>>>> --glmdirlh.grp2.pet.thickness.glmdir
> >>> >>>>> mri_glmfit --yrh.pvr_grp2_pet.nii.gz
> >>> --fsgd > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > >>> >>>>> rh_pvr_grp2_thickness.mgh --surf fsaverage lh > >>> --cortex > >>> >>>>> --glmdirrh.grp2.pet.thickness.glmdir
> >>> >>>>> > >>> >>>>> My questions. > >>> >>>>> 1) will my fsgd file contain > both groups? > >>> >>>>> 2) If the answer from question > is yes, > >>> i should have 2 > >>> >>>>> contrasts (pvr1.mtx for group1 and > >>> pvr2.mtx for > >>> >>>>> group2). yes/no? > >>> >>>>> 3) below is a sample of my fsgd > file. > >>> are the > >>> >>>>> constrasts correct? > >>> >>>>> > >>> >>>>> Thank you very much. > >>> >>>>> Paul. > >>> >>>>> The fsgd file lists: > >>> >>>>> > >>> ------------------------------------------------------------- > >>> >>>>> GroupDescriptorFile 1 > >>> >>>>> Title Relationship Amy-thick reg out > >>> age and education > >>> >>>>> Class g1 > >>> >>>>> Class g2 > >>> >>>>> Variable Age Education > >>> >>>>> Input XX1 g1 60 16 > >>> >>>>> Input YY1 g2 62 20 > >>> >>>>> > >>> ------------------------------------------------------------- > >>> >>>>> matrix for group1: > >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 > >>> >>>>> is there a relationship between > >>> amyloid-thickness in group1 regressing out age > >>> >>>>> and education? > >>> >>>>> matrix for group2: > >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 > >>> >>>>> is there a relationship between > >>> amyloid-thickness in group2 regressing out age > >>> >>>>> and education? > >>> >>>>> > >>> >>>>> On Thu, Aug 1, 2019 at 9:44 PM > Greve, > >>> Douglas N.,Ph.D. > >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > >>> >>>>> > >>> >>>>> Each PVR adds a single column to > >>> the design > >>> >>>>> matrix. In a two group design, > >>> this can make it > >>> >>>>> tricky to set up. Let's say you > >>> have 10 of group1 > >>> >>>>> and 20 of group2. You will need to > >>> create two PVR > >>> >>>>> files, each with 30=10+20 frames. > >>> In the first > >>> >>>>> one, the first 10 frames will be > >>> cortical > >>> >>>>> thickness (or amyloid sampled on > >>> the surface) of > >>> >>>>> group1; the next 20 frames will be > >>> all zeros. For > >>> >>>>> the 2nd PVR, the first 10 frames > >>> will be 0s and > >>> >>>>> the next 20 frames will be the > >>> cortical thickness > >>> >>>>> (or amyloid) for group2. I would > >>> start by running > >>> >>>>> mris_preproc for the two groups separate (so 2 > >>> >>>>> files, one with 10 frames the > >>> other 20 frames). > >>> >>>>> Then create the file of zeros using > >>> >>>>> fscalc group2.mgz mul 0 -o > >>> group2.zeros.mgz > >>> >>>>> Then > >>> >>>>> mri_concat group1.mgz group2.zeros.mgz --o > pvr1.mgz > >>> >>>>> Then create the contrast based on > >>> the FSGD, but > >>> >>>>> then add two more numbers, one for > >>> PVR1 (which > >>> >>>>> tests for the within group > >>> correlation), and one > >>> >>>>> for PVR2 > >>> >>>>> > >>> >>>>> > >>> >>>>> On 8/1/2019 3:14 PM, miracle > >>> ozzoude wrote: > >>> >>>>>> > >>> >>>>>> External Email - UseCaution
> >>> >>>>>> > >>> >>>>>> Please, can anyone help me with this. > >>> >>>>>> Thank you > >>> >>>>>> > >>> >>>>>> Paul > >>> >>>>>> > >>> >>>>>> ---------- Forwarded message --------- > >>> >>>>>> From: *miracle ozzoude* > >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> > >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11PM
> >>> >>>>>> Subject: multimodal analysis (pet and cortical > >>> >>>>>> thickness relationship) using --pvr > >>> >>>>>> To: Douglas N Greve > >>> >>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > >>> >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > >>> >>>>>> > >>> >>>>>> > >>> >>>>>> Hello Experts, > >>> >>>>>> > >>> >>>>>> I am performing an analysis > >>> looking at the > >>> >>>>>> relationship between amyloid uptake and > cortical > >>> >>>>>> thickness using --pvr flag in mri_glmfit. > I've 2 > >>> >>>>>> groups and 2 variables (age and education). I > >>> >>>>>> want to run a within group > >>> analysis while > >>> >>>>>> regressing out age and education (i.e. Within > >>> >>>>>> group 1, is there a negative > >>> relationship between > >>> >>>>>> amyloid uptake and cortical thickness > regressing > >>> >>>>>> out the effects of age and > >>> education). > >>> >>>>>> > >>> >>>>>> However, i'm not sure how my pvr contrasts > will > >>> >>>>>> look like. Below are my fsgd and > >>> an attempt at > >>> >>>>>> creating contrasts. Please, can you let me > know > >>> >>>>>> if my contrasts are correct based > >>> on my questions. > >>> >>>>>> > >>> >>>>>> Thank you. > >>> >>>>>> > >>> >>>>>> Best, > >>> >>>>>> Paul > >>> >>>>>> > >>> >>>>>> The fsgd file lists: > >>> >>>>>> > >>> ------------------------------------------------------------- > >>> >>>>>> GroupDescriptorFile 1 > >>> >>>>>> Title Relationship Amy-thick reg > >>> out age and education > >>> >>>>>> Class g1 > >>> >>>>>> Class g2 > >>> >>>>>> Variable Age Education > >>> >>>>>> Input XX1 g1 60 16 > >>> >>>>>> Input XX2 g1 58 14 > >>> >>>>>> Input YY1 g2 62 20 > >>> >>>>>> �� Input YY1 g2 62 20 > >>> >>>>>> > >>> ------------------------------------------------------------- > >>> >>>>>> matrix for group1: > >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 > >>> >>>>>> is there a relationship between > >>> amyloid-thickness in group1 regressing out age > >>> >>>>>> and education? > >>> >>>>>> matrix for group2: > >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 > >>> >>>>>> is there a relationship between > >>> amyloid-thickness in group2 regressing out age > >>> >>>>>> and education? > >>> >>>>>> > >>> >>>>>> > >>> >>>>>> > >>> >>>>>> > >>> >>>>>> > _______________________________________________ > >>> >>>>>> Freesurfer mailing list > >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>>>> > >>> 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_______________________________________________ > >>> >>>>> Freesurfer mailing list > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >>>> > >>> >>>> _______________________________________________ > >>> >>>> Freesurfer mailing list > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >>>> > >>> >>>> > >>> >>>> _______________________________________________ > >>> >>>> Freesurfer mailing list > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >>> > >>> >>> > >>> >>> _______________________________________________ > >>> >>> Freesurfer mailing list > >>> >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >> > >>> >> _______________________________________________ > >>> >> Freesurfer mailing list > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> >> > >>> >> > >>> >> _______________________________________________ > >>> >> Freesurfer mailing list > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> >> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >>> > > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> 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1:08 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
Then just do the standard PETsurfer processing
On 8/14/19 12:59 PM, miracle ozzoude wrote:
External Email - Use Caution
I want to use the aparc ROI. something similar to doing ROI surface base cortical thickness analysis where i used mri_annotation2label to extract the regions and mri_mergelabels to merge them and run analysis on them.
On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Do you mean using different ROIs than in the aparc? If you want to use the aparc, then that is done in the standard processing. On 8/14/19 11:16 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Hey Doug, > > If i want to do ROI surface base PET analysis using the method on the > PETsurfer website. Please, how do i go about doing it? I know there > series of commands i will need to run before project it to the surface > using mri_vol2surf. > thanks a lot > best, > Paul > > On Tue, Aug 13, 2019 at 11:00 AM miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> wrote: > > Awesome. thanks a lot for your help. I appreciate it. > > Best, > Paul > > On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > You can use mri_surfcluster. That actually has an --fdr flag, > so you > should not need to run mri_fdr. When you use --fdr, you do not > use > --thmin. Use --sum to get the summary file > > On 8/13/19 10:50 AM, miracle ozzoude wrote: > > > > External Email - Use Caution > > > > Thanks a lot doug. I want to use mri_fdr instead of > mri_glmfit-sim. > > How do i get a summary of clusters like mri_glmfit-sim? I > searched > > through the forum and based on previous responses, The > advice was to > > do mri_fdr and then use mri_surfcluster without the fdr > option to > > obtain the summary of cluster. Is this correct? > > Paul > > > > On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: > > > > I don't know that there is much you can do. The PVR is very > > computationally intensive, and it does not surprise me > that it is > > taking > > a long time. I don't think you need to do 10k > permutations. I would > > start with 1k. In the output, you will get a confidence > interval > > for the > > corrected p-value. This will shrink with the number of > > permutations, but > > if you're happy with it, no need to do more > > > > On 8/13/19 10:17 AM, miracle ozzoude wrote: > > > > > > External Email - Use Caution > > > > > > Thanks Doug. My correction for multiple comparison > using 10000 > > > permutation and abs has been running for 3days. This > is strange > > > because i am using the --bg 10 and it usually takes > 1hr to finish > > > without the --pvr. how do i solve this? > > > Below is my mri_glmfit and mri_glmfit-sim commands > > > > > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd > dods --C $pvr1 > > > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > > > --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf > > fsaverage lh > > > --cortex \ > > > --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save > > > > > > mri_glmfit-sim --glmdir > ${wholebrain}/lh.pet.thickness.glmdir > > --perm > > > 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 > --overwrite > > > > > > > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > wrote: > > > > > > You will have to click on the vertex you are > interested in. The > > > value will be -log10(pcorrected) where pcorrected > is the > > corrected > > > p-value > > > > > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: > > >> > > >> External Email - Use Caution > > >> > > >> these regions (please see below) came out > significant for the > > >> voxel-wise corrected map. I want to know their > p-values. > > >> mri-glmfit-sim doesn't give summary file for > voxel-wise > > corrected > > >> map only for cluster-wise map. > > >> image.png > > >> > > >> On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas > N.,Ph.D. > > >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > wrote: > > >> > > >> I'm not sure what you are looking for. The > voxel-wise > > >> analysis is voxel-wise, so there is no > summary file for it > > >> > > >> On 8/12/2019 11:13 AM, miracle ozzoude wrote: > > >>> > > >>> External Email - Use Caution > > >>> > > >>> Thanks Doug. Another question, how do i find > the p-values > > >>> for voxel-wise map corrected for multiple > comparisons at a > > >>> voxel (rather than cluster) level > > >>> (perm.th40.abs.sig.voxel.mgh). There is no summary > > file for it. > > >>> Best, > > >>> Paul > > >>> > > >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, > Douglas N.,Ph.D. > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > > >>> > > >>> The 3 spaces is for left hemi, right > hemi, and > > >>> subcortical, so, if you > > >>> are using all three then correct for all 3 > > >>> > > >>> On 8/7/19 9:26 AM, miracle ozzoude wrote: > > >>> > > > >>> > External Email - Use Caution > > >>> > > > >>> > Got it. Thanks a lot doug. If i have > to correct for > > >>> multiple > > >>> > comparison in surface based pet > analysis and > > >>> mutlimodal analysis (pet > > >>> > and thickness), should i use --3spaces? > > >>> > Thank you. > > >>> > > > >>> > best, > > >>> > Paul > > >>> > > > >>> > On Mon, Aug 5, 2019 at 10:19 PM Greve, > Douglas > > N.,Ph.D. > > >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > >>> > > > >>> > I think there is still something > not right. You > > >>> should just have > > >>> > one mri_glmfit command for each > hemisphere in > > >>> which the input is > > >>> > ?h.thickness.15.mgh, the fsgdfile is > > project.fsgd, > > >>> you then > > >>> > specify the pvrs for both groups > (--pvr > > >>> ?h.pvr_grp1_pet.nii.gz > > >>> > --pvr ?h.pvr_grp2_pet.niigz) and > then use that > > >>> first contrast. The > > >>> > second is the same as the first > but with a > > >>> reversed sign, but it > > >>> > is not necessary since we always > use unsigned > > >>> tests and show both > > >>> > signs (but you can still do it). > > >>> > > > >>> > On 8/5/2019 8:14 PM, miracle > ozzoude wrote: > > >>> >> > > >>> >> External Email - Use Caution > > >>> >> > > >>> >> I think i got it now. Something > like this: > > >>> >> > > >>> >> ## group1 comes first in my fsgd > file. removing > > >>> the effects of > > >>> >> age and education > > >>> >> ##amyloid-thickness. first pet pvr = > 1 for > > group1 > > >>> and 0 for group 2. > > >>> >> mri_glmfit --y > lh.thickness.15.mgh --fsgd > > >>> project.fsgd dods --c > > >>> >> pvr1.mtx --pvr > lh.pvr_grp1_pet.nii.gz \ > > >>> >> --pvr > > >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > >>> >> fsaverage lh --cortex --glmdir > > >>> lh.pet.thickness.glmdir > > >>> >> mri_glmfit --y > rh.thickness.15.mgh --fsgd > > >>> project.fsgd dods --c > > >>> >> pvr1.mtx --pvr > rh.pvr_grp1_pet.nii.gz \ > > >>> >> --pvr > > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > fsaverage > > >>> >> lh --cortex --glmdir > rh.pet.thickness.glmdir > > >>> >> > > >>> >> contrast = 0 0 0 0 0 0 1 -1 > > >>> >> > > >>> >> ##group 2 is second in my fsgd file. > > removing the > > >>> effects of age > > >>> >> and education > > >>> >> ##amyloid-thickness. first pet pvr = > 0 for > > group1 > > >>> and 1 for group2 > > >>> >> mri_glmfit --y > lh.thickness.15.mgh --fsgd > > >>> project.fsgd dods --c > > >>> >> pvr2.mtx --pvr > > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > >>> >> --pvr lh.pvr_grp2_pet.nii.gz > -surf fsaverage lh > > >>> --cortex --glmdir > > >>> >> rh.pet.thickness.glmdir > > >>> >> mri_glmfit --y > rh.thickness.15.mgh --fsgd > > >>> project.fsgd dods --c > > >>> >> pvr2.mtx --pvr > > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > >>> >> --pvr rh.pvr_grp2_pet.nii.gz > -surf fsaverage lh > > >>> --cortex --glmdir > > >>> >> rh.pet.thickness.glmdir > > >>> >> > > >>> >> contrast = 0 0 0 0 0 0 -1 1 > > >>> >> > > >>> >> On Mon, Aug 5, 2019 at 6:47 PM > Greve, Douglas > > >>> N.,Ph.D. > > >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > >>> >> > > >>> >> It still looks like you are > using a group > > >>> specific input > > >>> >> (--y). The input should be a > simple > > file with > > >>> both groups > > >>> >> (same input as you would use > without pvr) > > >>> >> > > >>> >> On 8/5/2019 4:39 PM, > miracooloz wrote: > > >>> >>> > > >>> >>> External Email - Use Caution > > >>> >>> > > >>> >>> Thanks Doug. How about the mri_glmfit > > >>> commands? Since the > > >>> >>> contrasts are correct, I think the > > commands > > >>> should be right. > > >>> >>> > > >>> >>> Best, > > >>> >>> Paul. > > >>> >>> > > >>> >>> > > >>> >>> > > >>> >>> Sent from my Samsung Galaxy smartphone. > > >>> >>> > > >>> >>> -------- Original message -------- > > >>> >>> From: "Greve, Douglas N.,Ph.D." > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > >>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > >>> >>> Date: 2019-08-05 15:52 (GMT-05:00) > > >>> >>> To: > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>> Subject: Re: [Freesurfer] Fwd: > multimodal > > >>> analysis (pet and > > >>> >>> cortical thickness relationship) using > > --pvr > > >>> >>> > > >>> >>> Yes, that contrast is correct. > > >>> >>> > > >>> >>> On 8/5/2019 3:11 PM, miracle > ozzoude > > wrote: > > >>> >>>> > > >>> >>>> External Email - Use Caution > > >>> >>>> > > >>> >>>> Hello Doug, > > >>> >>>> > > >>> >>>> Thanks very much for your help. Your > > >>> assumption was right > > >>> >>>> in that i want to run a group > comparison > > >>> (i.e. test for a > > >>> >>>> difference in amyloid-thickness slopes > > >>> between the two > > >>> >>>> groups). However, I am having a > hard time > > >>> creating the > > >>> >>>> correct mri_glmfit and contrasts > in this > > >>> case. Based on > > >>> >>>> your advice and searching through the > > forum > > >>> >>>> > > >>> > > > (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i > > >>> >>>> need 2 PVRs for each hemisphere in the > > >>> mri_glmfit command. > > >>> >>>> I gave it another shot below. Please > > let me > > >>> know if i am > > >>> >>>> correct. > > >>> >>>> > > >>> >>>> Thank you. > > >>> >>>> Paul. > > >>> >>>> > > >>> >>>> ## group1 comes first in my fsgd file. > > >>> removing the effects > > >>> >>>> of age and education > > >>> >>>> ##amyloid-thickness. first pet pvr > = 1 for > > >>> group1 and 0 for > > >>> >>>> group 2. > > >>> >>>> mri_glmfit --y > > lh_pvr_grp1_thickness.mgh --fsgd > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > >>> lh.pvr_grp1_pet.nii.gz \ > > >>> >>>> --pvr > > >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > >>> >>>> fsaverage lh --cortex --glmdir > > >>> lh.pet.thickness.glmdir > > >>> >>>> mri_glmfit --y > > rh_pvr_grp1_thickness.mgh --fsgd > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > >>> rh.pvr_grp1_pet.nii.gz \ > > >>> >>>> --pvr > > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > >>> >>>> fsaverage lh --cortex --glmdir > > >>> rh.pet.thickness.glmdir > > >>> >>>> > > >>> >>>> contrast = 0 0 0 0 0 0 1 -1 > > >>> >>>> > > >>> >>>> ##group 2 is second in my fsgd file. > > >>> removing the effects > > >>> >>>> of age and education > > >>> >>>> ##amyloid-thickness. first pet pvr > = 0 for > > >>> group1 and 1 for > > >>> >>>> group2 > > >>> >>>> mri_glmfit --y > > >>> lh_pvr_grp2_thickness.mgh --fsgd > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > >>> >>>> > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf > > >>> fsaverage lh --cortex > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > >>> >>>> mri_glmfit --y > > rh_pvr_grp2_thickness.mgh --fsgd > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > >>> >>>> > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf > > >>> fsaverage lh --cortex > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > >>> >>>> > > >>> >>>> contrast = 0 0 0 0 0 0 -1 1 > > >>> >>>> > > >>> >>>> > > >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, > > >>> Douglas N.,Ph.D. > > >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > >>> >>>> > > >>> >>>> That mostly looks good. > > >>> >>>> > > >>> >>>> I would suggest is to change your > > >>> smoothing command to > > >>> >>>> something like > > >>> >>>> mris_fwhm --smooth-only --s fsaverage > > >>> --hemi lh --fwhm > > >>> >>>> 5 --cortex --prune --i > > >>> >>>> > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>> The only difference will be > that any > > >>> vertices that are > > >>> >>>> 0 in the input will be excluded > > >>> (pruned) from the > > >>> >>>> smoothing mask. > > >>> >>>> > > >>> >>>> The mri_glmfit command is not > right. > > >>> That command looks > > >>> >>>> like it is for analyzing each > group > > >>> separately and > > >>> >>>> independently. If that is what you > want > > >>> to do, then you > > >>> >>>> don't need to go through all the > > extra > > >>> stuff of > > >>> >>>> creating zero files, etc. I had > > assumed > > >>> that you wanted > > >>> >>>> to do some kind of comparison > between > > >>> groups. If so, > > >>> >>>> then you would use a single > file with > > >>> all your data in > > >>> >>>> it (probably what you were using > > >>> before), and your fsgd > > >>> >>>> file would have both groups. > > >>> >>>> > > >>> >>>> 1) will my fsgd file contain both > > groups? > > >>> >>>> yes, see above > > >>> >>>> 2) If the answer from question is > > yes, > > >>> i should have 2 > > >>> >>>> contrasts (pvr1.mtx for group1 and > > >>> pvr2.mtx for > > >>> >>>> group2). yes/no? > > >>> >>>> Again, if all you want to do is > > to test > > >>> the pvr for > > >>> >>>> each group separately, then > you don't > > >>> need to go > > >>> >>>> through the processes of creating > > zero > > >>> files, etc. In > > >>> >>>> any event, if you want to test > a pvr, > > >>> then you need a > > >>> >>>> contrast for it. > > >>> >>>> 3) below is a sample of my > fsgd file. > > >>> are the > > >>> >>>> constrasts correct? > > >>> >>>> hard to say without resolving the > > >>> questions above. You > > >>> >>>> will need to have a value in the > > >>> contrast for each pvr. > > >>> >>>> > > >>> >>>> > > >>> >>>> > > >>> >>>> On 8/2/2019 3:56 PM, miracle > > ozzoude wrote: > > >>> >>>>> > > >>> >>>>> External Email - Use Caution > > >>> >>>>> > > >>> >>>>> Hello Doug, > > >>> >>>>> > > >>> >>>>> Thanks for answering. Based on your > > >>> explanation, i > > >>> >>>>> wrote out a series of command needed > > >>> to execute this. > > >>> >>>>> Please let me know if i made any > > >>> mistakes/correct. > > >>> >>>>> ##step1 concatenating the 10 amyloid > > >>> pet volumes files > > >>> >>>>> projected to surface using > > >>> mri_vol2surf for group1 > > >>> >>>>> mri_concat --f grp1.lhmgxctx --o > > >>> >>>>> > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > >>> >>>>> > allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > > >>> >>>>> > > >>> >>>>> ##step2 concatenating the 20 amyloid > > >>> pet volumes files > > >>> >>>>> projected to surface using > > >>> mri_vol2surf for group2 > > >>> >>>>> mri_concat --f grp2.lhmgxctx --o > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > >>> >>>>> > allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > > >>> >>>>> > > >>> >>>>> ##step3 smooth on the surface for > each > > >>> hemisphere for > > >>> >>>>> group1 > > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > > >>> --sval > > >>> >>>>> > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > >>> >>>>> --cortex --tval > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > > >>> --sval > > >>> >>>>> > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > --fwhm 5 > > >>> >>>>> --cortex --tval > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> > > >>> >>>>> ##step4 smooth on the surface for > each > > >>> hemisphere for > > >>> >>>>> group2 > > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > > >>> --sval > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > >>> >>>>> --cortex --tval > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > > >>> --sval > > >>> >>>>> > allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz > > --fwhm 5 > > >>> >>>>> --cortex --tval > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> > > >>> >>>>> ##step5 create files of zeros for > > >>> group1 for each > > >>> >>>>> hemisphere > > >>> >>>>> fscalc > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > >>> >>>>> > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> fscalc > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > >>> >>>>> > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> > > >>> >>>>> ##step6 create files of zeros for > > >>> group2 for each > > >>> >>>>> hemisphere > > >>> >>>>> fscalc > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> fscalc > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > >>> >>>>> > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> > > >>> >>>>> ##step7 create pvr files for group1 > > >>> for each hemisphere > > >>> >>>>> mri_concat > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > > >>> >>>>> lh.pvr_grp1_pet.nii.gz > > >>> >>>>> mri_concat > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > > >>> >>>>> rh.pvr_grp1_pet.nii.gz > > >>> >>>>> > > >>> >>>>> ##step8 create pvr files for group2 > > >>> for each hemisphere > > >>> >>>>> mri_concat > > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > > >>> >>>>> lh.pvr_grp2_pet.nii.gz > > >>> >>>>> mri_concat > > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> > allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > > >>> >>>>> rh.pvr_grp2_pet.nii.gz > > >>> >>>>> > > >>> >>>>> ###-----repeat steps 1-8 for > cortical > > >>> thickness------- > > >>> >>>>> > > >>> >>>>> ###run glm-fit for group1 > > >>> >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz > > >>> --fsgd > > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > > >>> >>>>> lh_pvr_grp1_thickness.mgh --surf > fsaverage lh > > >>> --cortex > > >>> >>>>> --glmdir lh.grp1.pet.thickness.glmdir > > >>> >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz > > >>> --fsgd > > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > > >>> >>>>> rh_pvr_grp1_thickness.mgh --surf > fsaverage lh > > >>> --cortex > > >>> >>>>> --glmdir rh.grp1.pet.thickness.glmdir > > >>> >>>>> > > >>> >>>>> ###run glm-fit for group2 > > >>> >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz > > >>> --fsgd > > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > > >>> >>>>> lh_pvr_grp2_thickness.mgh --surf > fsaverage lh > > >>> --cortex > > >>> >>>>> --glmdir lh.grp2.pet.thickness.glmdir > > >>> >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz > > >>> --fsgd > > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > > >>> >>>>> rh_pvr_grp2_thickness.mgh --surf > fsaverage lh > > >>> --cortex > > >>> >>>>> --glmdir rh.grp2.pet.thickness.glmdir > > >>> >>>>> > > >>> >>>>> My questions. > > >>> >>>>> 1) will my fsgd file contain > > both groups? > > >>> >>>>> 2) If the answer from > question > > is yes, > > >>> i should have 2 > > >>> >>>>> contrasts (pvr1.mtx for group1 and > > >>> pvr2.mtx for > > >>> >>>>> group2). yes/no? > > >>> >>>>> 3) below is a sample of > my fsgd > > file. > > >>> are the > > >>> >>>>> constrasts correct? > > >>> >>>>> > > >>> >>>>> Thank you very much. > > >>> >>>>> Paul. > > >>> >>>>> The fsgd file lists: > > >>> >>>>> > > >>> > ------------------------------------------------------------- > > >>> >>>>> GroupDescriptorFile 1 > > >>> >>>>> Title Relationship Amy-thick reg out > > >>> age and education > > >>> >>>>> Class g1 > > >>> >>>>> Class g2 > > >>> >>>>> Variable Age Education > > >>> >>>>> Input XX1 g1 60 16 > > >>> >>>>> Input YY1 g2 62 20 > > >>> >>>>> > > >>> > ------------------------------------------------------------- > > >>> >>>>> matrix for group1: > > >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 > > >>> >>>>> is there a relationship > between > > >>> amyloid-thickness in group1 regressing > out age > > >>> >>>>> and education? > > >>> >>>>> matrix for group2: > > >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 > > >>> >>>>> is there a relationship > between > > >>> amyloid-thickness in group2 regressing > out age > > >>> >>>>> and education? > > >>> >>>>> > > >>> >>>>> On Thu, Aug 1, 2019 at > 9:44 PM > > Greve, > > >>> Douglas N.,Ph.D. > > >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > >>> >>>>> > > >>> >>>>> Each PVR adds a single column to > > >>> the design > > >>> >>>>> matrix. In a two group design, > > >>> this can make it > > >>> >>>>> tricky to set up. Let's say you > > >>> have 10 of group1 > > >>> >>>>> and 20 of group2. You will need to > > >>> create two PVR > > >>> >>>>> files, each with 30=10+20 frames. > > >>> In the first > > >>> >>>>> one, the first 10 frames will be > > >>> cortical > > >>> >>>>> thickness (or amyloid sampled on > > >>> the surface) of > > >>> >>>>> group1; the next 20 frames will be > > >>> all zeros. For > > >>> >>>>> the 2nd PVR, the first 10 frames > > >>> will be 0s and > > >>> >>>>> the next 20 frames will be the > > >>> cortical thickness > > >>> >>>>> (or amyloid) for group2. I would > > >>> start by running > > >>> >>>>> mris_preproc for the two groups > separate (so 2 > > >>> >>>>> files, one with 10 frames the > > >>> other 20 frames). > > >>> >>>>> Then create the file of zeros using > > >>> >>>>> fscalc group2.mgz mul 0 -o > > >>> group2.zeros.mgz > > >>> >>>>> Then > > >>> >>>>> mri_concat group1.mgz > group2.zeros.mgz --o > > pvr1.mgz > > >>> >>>>> Then create the contrast based on > > >>> the FSGD, but > > >>> >>>>> then add two more numbers, one for > > >>> PVR1 (which > > >>> >>>>> tests for the within group > > >>> correlation), and one > > >>> >>>>> for PVR2 > > >>> >>>>> > > >>> >>>>> > > >>> >>>>> On 8/1/2019 3:14 PM, miracle > > >>> ozzoude wrote: > > >>> >>>>>> > > >>> >>>>>> External Email - Use Caution > > >>> >>>>>> > > >>> >>>>>> Please, can anyone help me with > this. > > >>> >>>>>> Thank you > > >>> >>>>>> > > >>> >>>>>> Paul > > >>> >>>>>> > > >>> >>>>>> ---------- Forwarded message > --------- > > >>> >>>>>> From: *miracle ozzoude* > > >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>>> > > >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM > > >>> >>>>>> Subject: multimodal analysis > (pet and cortical > > >>> >>>>>> thickness relationship) using --pvr > > >>> >>>>>> To: Douglas N Greve > > >>> >>>>>> > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >>>>>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>> > > >>> >>>>>> > > >>> >>>>>> > > >>> >>>>>> Hello Experts, > > >>> >>>>>> > > >>> >>>>>> I am performing an analysis > > >>> looking at the > > >>> >>>>>> relationship between amyloid > uptake and > > cortical > > >>> >>>>>> thickness using --pvr flag in > mri_glmfit. > > I've 2 > > >>> >>>>>> groups and 2 variables (age and > education). I > > >>> >>>>>> want to run a within group > > >>> analysis while > > >>> >>>>>> regressing out age and education > (i.e. Within > > >>> >>>>>> group 1, is there a negative > > >>> relationship between > > >>> >>>>>> amyloid uptake and cortical > thickness > > regressing > > >>> >>>>>> out the effects of age and > > >>> education). > > >>> >>>>>> > > >>> >>>>>> However, i'm not sure how my pvr > contrasts > > will > > >>> >>>>>> look like. Below are my fsgd and > > >>> an attempt at > > >>> >>>>>> creating contrasts. Please, can > you let me > > know > > >>> >>>>>> if my contrasts are correct based > > >>> on my questions. > > >>> >>>>>> > > >>> >>>>>> Thank you. > > >>> >>>>>> > > >>> >>>>>> Best, > > >>> >>>>>> Paul > > >>> >>>>>> > > >>> >>>>>> The fsgd file lists: > > >>> >>>>>> > > >>> > ------------------------------------------------------------- > > >>> >>>>>> GroupDescriptorFile 1 > > >>> >>>>>> Title Relationship Amy-thick reg > > >>> out age and education > > >>> >>>>>> Class g1 > > >>> >>>>>> Class g2 > > >>> >>>>>> Variable Age Education > > >>> >>>>>> Input XX1 g1 60 16 > > >>> >>>>>> Input XX2 g1 58 14 > > >>> >>>>>> Input YY1 g2 62 20 > > >>> >>>>>> �� Input YY1 g2 62 20 > > >>> >>>>>> > > >>> > ------------------------------------------------------------- > > >>> >>>>>> matrix for group1: > > >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 > > >>> >>>>>> is there a relationship between > > >>> amyloid-thickness in group1 regressing > out age > > >>> >>>>>> and education? > > >>> >>>>>> matrix for group2: > > >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 > > >>> >>>>>> is there a relationship between > > >>> amyloid-thickness in group2 regressing > out age > > >>> >>>>>> and education? > > >>> >>>>>> > > >>> >>>>>> > > >>> >>>>>> > > >>> >>>>>> > > >>> >>>>>> > > _______________________________________________ > > >>> >>>>>> Freesurfer mailing list > > >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>>>> > > >>> >>>>> > _______________________________________________ > > >>> >>>>> Freesurfer mailing list > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >>>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>>>> > > >>> >>>>> > > >>> >>>>> > _______________________________________________ > > >>> >>>>> Freesurfer mailing list > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>>> > > >>> >>>> > _______________________________________________ > > >>> >>>> Freesurfer mailing list > > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>>> > > >>> >>>> > > >>> >>>> > _______________________________________________ > > >>> >>>> Freesurfer mailing list > > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>> > > >>> >>> > > >>> >>> > _______________________________________________ > > >>> >>> Freesurfer mailing list > > >>> >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >> > > >>> >> > _______________________________________________ > > >>> >> Freesurfer mailing list > > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >> > > >>> >> > > >>> >> > _______________________________________________ > > >>> >> Freesurfer mailing list > > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > > >>> > > _______________________________________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> > > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > > >>> > > > >>> > > _______________________________________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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1:15 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
the surface based pet analysis in the petsurfer link use the whole brain. i want to do my surface base pet analysis on specific regions of the aparc not the entire regions. Should i use mri_vol2label to extract the covert the volume to labels, them mri_mergelabels to merge them? Thanks.
On Wed, Aug 14, 2019 at 1:08 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Then just do the standard PETsurfer processing
On 8/14/19 12:59 PM, miracle ozzoude wrote:
External Email - Use CautionI want to use the aparc ROI. something similar to doing ROI surface base cortical thickness analysis where i used mri_annotation2label to extract the regions and mri_mergelabels to merge them and run analysis on them.
On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Do you mean using different ROIs than in the aparc? If you want to use the aparc, then that is done in the standard processing. On 8/14/19 11:16 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Hey Doug, > > If i want to do ROI surface base PET analysis using the method on the > PETsurfer website. Please, how do i go about doing it? I know there > series of commands i will need to run before project it to the surface > using mri_vol2surf. > thanks a lot > best, > Paul > > On Tue, Aug 13, 2019 at 11:00 AM miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>wrote:
> > Awesome. thanks a lot for your help. I appreciate it. > > Best, > Paul > > On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > You can use mri_surfcluster. That actually has an --fdr flag, > so you > should not need to run mri_fdr. When you use --fdr, you do not > use > --thmin. Use --sum to get the summary file > > On 8/13/19 10:50 AM, miracle ozzoude wrote: > > > > External Email - Use Caution > > > > Thanks a lot doug. I want to use mri_fdr instead of > mri_glmfit-sim. > > How do i get a summary of clusters like mri_glmfit-sim? I > searched > > through the forum and based on previous responses, The > advice was to > > do mri_fdr and then use mri_surfcluster without the fdr > option to > > obtain the summary of cluster. Is this correct? > > Paul > > > > On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> wrote: > > > > I don't know that there is much you can do. The PVR is very > > computationally intensive, and it does not surpriseme
> that it is > > taking > > a long time. I don't think you need to do 10k > permutations. I would > > start with 1k. In the output, you will get a confidence > interval > > for the > > corrected p-value. This will shrink with the numberof
> > permutations, but > > if you're happy with it, no need to do more > > > > On 8/13/19 10:17 AM, miracle ozzoude wrote: > > > > > > External Email - Use Caution > > > > > > Thanks Doug. My correction for multiple comparison > using 10000 > > > permutation and abs has been running for 3days.This
> is strange > > > because i am using the --bg 10 and it usually takes > 1hr to finish > > > without the --pvr. how do i solve this? > > > Below is my mri_glmfit and mri_glmfit-sim commands > > > > > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd > dods --C $pvr1 > > > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh\
> > > --pvr ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf > > fsaverage lh > > > --cortex \ > > > --glmdir ${wholebrain}/lh.pet.thickness.glmdir --eres-save > > > > > > mri_glmfit-sim --glmdir > ${wholebrain}/lh.pet.thickness.glmdir > > --perm > > > 10000 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 > --overwrite > > > > > > > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D. > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > wrote: > > > > > > You will have to click on the vertex you are > interested in. The > > > value will be -log10(pcorrected) where pcorrected > is the > > corrected > > > p-value > > > > > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: > > >> > > >> External Email - Use Caution > > >> > > >> these regions (please see below) came out > significant for the > > >> voxel-wise corrected map. I want to know their > p-values. > > >> mri-glmfit-sim doesn't give summary file for > voxel-wise > > corrected > > >> map only for cluster-wise map. > > >> image.png > > >> > > >> On Mon, Aug 12, 2019 at 11:19 AM Greve,Douglas
> N.,Ph.D. > > >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > wrote: > > >> > > >> I'm not sure what you are looking for. The > voxel-wise > > >> analysis is voxel-wise, so there is no > summary file for it > > >> > > >> On 8/12/2019 11:13 AM, miracle ozzoude wrote: > > >>> > > >>> External Email - Use Caution > > >>> > > >>> Thanks Doug. Another question, how do i find > the p-values > > >>> for voxel-wise map corrected for multiple > comparisons at a > > >>> voxel (rather than cluster) level > > >>> (perm.th40.abs.sig.voxel.mgh). There is no summary > > file for it. > > >>> Best, > > >>> Paul > > >>> > > >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, > Douglas N.,Ph.D. > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > > >>> > > >>> The 3 spaces is for left hemi, right > hemi, and > > >>> subcortical, so, if you > > >>> are using all three then correct for all 3 > > >>> > > >>> On 8/7/19 9:26 AM, miracle ozzoude wrote: > > >>> > > > >>> > External Email - UseCaution
> > >>> > > > >>> > Got it. Thanks a lot doug. If ihave
> to correct for > > >>> multiple > > >>> > comparison in surface based pet > analysis and > > >>> mutlimodal analysis (pet > > >>> > and thickness), should i use --3spaces? > > >>> > Thank you. > > >>> > > > >>> > best, > > >>> > Paul > > >>> > > > >>> > On Mon, Aug 5, 2019 at 10:19 PM Greve, > Douglas > > N.,Ph.D. > > >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > >>> > > > >>> > I think there is stillsomething
> not right. You > > >>> should just have > > >>> > one mri_glmfit command for each > hemisphere in > > >>> which the input is > > >>> > ?h.thickness.15.mgh, the fsgdfile is > > project.fsgd, > > >>> you then > > >>> > specify the pvrs for both groups > (--pvr > > >>> ?h.pvr_grp1_pet.nii.gz > > >>> > --pvr ?h.pvr_grp2_pet.niigz)and
> then use that > > >>> first contrast. The > > >>> > second is the same as the first > but with a > > >>> reversed sign, but it > > >>> > is not necessary since wealways
> use unsigned > > >>> tests and show both > > >>> > signs (but you can still doit).
> > >>> > > > >>> > On 8/5/2019 8:14 PM, miracle > ozzoude wrote: > > >>> >> > > >>> >> External Email - Use Caution > > >>> >> > > >>> >> I think i got it now.Something
> like this: > > >>> >> > > >>> >> ## group1 comes first in my fsgd > file. removing > > >>> the effects of > > >>> >> age and education > > >>> >> ##amyloid-thickness. first pet pvr = > 1 for > > group1 > > >>> and 0 for group 2. > > >>> >> mri_glmfit --y > lh.thickness.15.mgh --fsgd > > >>> project.fsgd dods --c > > >>> >> pvr1.mtx --pvr > lh.pvr_grp1_pet.nii.gz \ > > >>> >> --pvr > > >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > >>> >> fsaverage lh --cortex --glmdir > > >>> lh.pet.thickness.glmdir > > >>> >> mri_glmfit --y > rh.thickness.15.mgh --fsgd > > >>> project.fsgd dods --c > > >>> >> pvr1.mtx --pvr > rh.pvr_grp1_pet.nii.gz \ > > >>> >> --pvr > > >>>allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf
> fsaverage > > >>> >> lh --cortex --glmdir > rh.pet.thickness.glmdir > > >>> >> > > >>> >> contrast = 0 0 0 0 0 0 1 -1 > > >>> >> > > >>> >> ##group 2 is second in my fsgd file. > > removing the > > >>> effects of age > > >>> >> and education > > >>> >> ##amyloid-thickness. first pet pvr = > 0 for > > group1 > > >>> and 1 for group2 > > >>> >> mri_glmfit --y > lh.thickness.15.mgh --fsgd > > >>> project.fsgd dods --c > > >>> >> pvr2.mtx --pvr > > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > >>> >> --pvr lh.pvr_grp2_pet.nii.gz > -surf fsaverage lh > > >>> --cortex --glmdir > > >>> >> rh.pet.thickness.glmdir > > >>> >> mri_glmfit --y > rh.thickness.15.mgh --fsgd > > >>> project.fsgd dods --c > > >>> >> pvr2.mtx --pvr > > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > >>> >> --pvr rh.pvr_grp2_pet.nii.gz > -surf fsaverage lh > > >>> --cortex --glmdir > > >>> >> rh.pet.thickness.glmdir > > >>> >> > > >>> >> contrast = 0 0 0 0 0 0 -1 1 > > >>> >> > > >>> >> On Mon, Aug 5, 2019 at 6:47 PM > Greve, Douglas > > >>> N.,Ph.D. > > >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > >>> >> > > >>> >> It still looks like you are > using a group > > >>> specific input > > >>> >> (--y). The input should be a > simple > > file with > > >>> both groups > > >>> >> (same input as you would use > without pvr) > > >>> >> > > >>> >> On 8/5/2019 4:39 PM, > miracooloz wrote: > > >>> >>> > > >>> >>> External Email - Use Caution > > >>> >>> > > >>> >>> Thanks Doug. How about the mri_glmfit > > >>> commands? Since the > > >>> >>> contrasts are correct, I think the > > commands > > >>> should be right. > > >>> >>> > > >>> >>> Best, > > >>> >>> Paul. > > >>> >>> > > >>> >>> > > >>> >>> > > >>> >>> Sent from my Samsung Galaxy smartphone. > > >>> >>> > > >>> >>> -------- Original message -------- > > >>> >>> From: "Greve, Douglas N.,Ph.D." > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > >>> >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > >>> >>> Date: 2019-08-05 15:52 (GMT-05:00) > > >>> >>> To: > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>> Subject: Re: [Freesurfer] Fwd: > multimodal > > >>> analysis (pet and > > >>> >>> cortical thickness relationship) using > > --pvr > > >>> >>> > > >>> >>> Yes, that contrast is correct. > > >>> >>> > > >>> >>> On 8/5/2019 3:11 PM, miracle > ozzoude > > wrote: > > >>> >>>> > > >>> >>>> External Email - Use Caution > > >>> >>>> > > >>> >>>> Hello Doug, > > >>> >>>> > > >>> >>>> Thanks very much for your help. Your > > >>> assumption was right > > >>> >>>> in that i want to run a group > comparison > > >>> (i.e. test for a > > >>> >>>> difference in amyloid-thickness slopes > > >>> between the two > > >>> >>>> groups). However, I am having a > hard time > > >>> creating the > > >>> >>>> correct mri_glmfit and contrasts > in this > > >>> case. Based on > > >>> >>>> your advice and searching through the > > forum > > >>> >>>> > > >>> > > > (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
> > >>> >>>> need 2 PVRs for each hemisphere in the > > >>> mri_glmfit command. > > >>> >>>> I gave it another shot below. Please > > let me > > >>> know if i am > > >>> >>>> correct. > > >>> >>>> > > >>> >>>> Thank you. > > >>> >>>> Paul. > > >>> >>>> > > >>> >>>> ## group1 comes first in my fsgd file. > > >>> removing the effects > > >>> >>>> of age and education > > >>> >>>> ##amyloid-thickness. first pet pvr > = 1 for > > >>> group1 and 0 for > > >>> >>>> group 2. > > >>> >>>> mri_glmfit --y > > lh_pvr_grp1_thickness.mgh --fsgd > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > >>> lh.pvr_grp1_pet.nii.gz \ > > >>> >>>> --pvr > > >>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > >>> >>>> fsaverage lh --cortex --glmdir > > >>> lh.pet.thickness.glmdir > > >>> >>>> mri_glmfit --y > > rh_pvr_grp1_thickness.mgh --fsgd > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > >>> rh.pvr_grp1_pet.nii.gz \ > > >>> >>>> --pvr > > >>>allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf
> > >>> >>>> fsaverage lh --cortex --glmdir > > >>> rh.pet.thickness.glmdir > > >>> >>>> > > >>> >>>> contrast = 0 0 0 0 0 0 1 -1 > > >>> >>>> > > >>> >>>> ##group 2 is second in my fsgd file. > > >>> removing the effects > > >>> >>>> of age and education > > >>> >>>> ##amyloid-thickness. first pet pvr > = 0 for > > >>> group1 and 1 for > > >>> >>>> group2 > > >>> >>>> mri_glmfit --y > > >>> lh_pvr_grp2_thickness.mgh --fsgd > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > >>> >>>> > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf > > >>> fsaverage lh --cortex > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > >>> >>>> mri_glmfit --y > > rh_pvr_grp2_thickness.mgh --fsgd > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > >>> >>>> > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf > > >>> fsaverage lh --cortex > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > >>> >>>> > > >>> >>>> contrast = 0 0 0 0 0 0 -1 1 > > >>> >>>> > > >>> >>>> > > >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, > > >>> Douglas N.,Ph.D. > > >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > >>> >>>> > > >>> >>>> That mostly looks good. > > >>> >>>> > > >>> >>>> I would suggest is to change your > > >>> smoothing command to > > >>> >>>> something like > > >>> >>>> mris_fwhm --smooth-only --s fsaverage > > >>> --hemi lh --fwhm > > >>> >>>> 5 --cortex --prune --i > > >>> >>>> > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>> The only difference will be > that any > > >>> vertices that are > > >>> >>>> 0 in the input will be excluded > > >>> (pruned) from the > > >>> >>>> smoothing mask. > > >>> >>>> > > >>> >>>> The mri_glmfit command is not > right. > > >>> That command looks > > >>> >>>> like it is for analyzing each > group > > >>> separately and > > >>> >>>> independently. If that is what you > want > > >>> to do, then you > > >>> >>>> don't need to go through all the > > extra > > >>> stuff of > > >>> >>>> creating zero files, etc. I had > > assumed > > >>> that you wanted > > >>> >>>> to do some kind of comparison > between > > >>> groups. If so, > > >>> >>>> then you would use a single > file with > > >>> all your data in > > >>> >>>> it (probably what you were using > > >>> before), and your fsgd > > >>> >>>> file would have both groups. > > >>> >>>> > > >>> >>>> 1) will my fsgd file contain both > > groups? > > >>> >>>> yes, see above > > >>> >>>> 2) If the answer from question is > > yes, > > >>> i should have 2 > > >>> >>>> contrasts (pvr1.mtx for group1 and > > >>> pvr2.mtx for > > >>> >>>> group2). yes/no? > > >>> >>>> Again, if all you want to do is > > to test > > >>> the pvr for > > >>> >>>> each group separately, then > you don't > > >>> need to go > > >>> >>>> through the processes of creating > > zero > > >>> files, etc. In > > >>> >>>> any event, if you want to test > a pvr, > > >>> then you need a > > >>> >>>> contrast for it. > > >>> >>>> 3) below is a sample of my > fsgd file. > > >>> are the > > >>> >>>> constrasts correct? > > >>> >>>> hard to say without resolving the > > >>> questions above. You > > >>> >>>> will need to have a value in the > > >>> contrast for each pvr. > > >>> >>>> > > >>> >>>> > > >>> >>>> > > >>> >>>> On 8/2/2019 3:56 PM, miracle > > ozzoude wrote: > > >>> >>>>> > > >>> >>>>> External Email - Use Caution > > >>> >>>>> > > >>> >>>>> Hello Doug, > > >>> >>>>> > > >>> >>>>> Thanks for answering. Based on your > > >>> explanation, i > > >>> >>>>> wrote out a series of command needed > > >>> to execute this. > > >>> >>>>> Please let me know if i made any > > >>> mistakes/correct. > > >>> >>>>> ##step1 concatenating the 10 amyloid > > >>> pet volumes files > > >>> >>>>> projected to surface using > > >>> mri_vol2surf for group1 > > >>> >>>>> mri_concat --f grp1.lhmgxctx --o > > >>> >>>>> > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > >>> >>>>> > allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > > >>> >>>>> > > >>> >>>>> ##step2 concatenating the 20 amyloid > > >>> pet volumes files > > >>> >>>>> projected to surface using > > >>> mri_vol2surf for group2 > > >>> >>>>> mri_concat --f grp2.lhmgxctx --o > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > >>> >>>>> > allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > > >>> >>>>> > > >>> >>>>> ##step3 smooth on the surface for > each > > >>> hemisphere for > > >>> >>>>> group1 > > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > > >>> --sval > > >>> >>>>> > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > >>> >>>>> --cortex --tval > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > > >>> --sval > > >>> >>>>> > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > --fwhm 5 > > >>> >>>>> --cortex --tval > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> > > >>> >>>>> ##step4 smooth on the surface for > each > > >>> hemisphere for > > >>> >>>>> group2 > > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > > >>> --sval > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > >>> >>>>> --cortex --tval > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > > >>> --sval > > >>> >>>>> > allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz > > --fwhm 5 > > >>> >>>>> --cortex --tval > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> > > >>> >>>>> ##step5 create files of zeros for > > >>> group1 for each > > >>> >>>>> hemisphere > > >>> >>>>> fscalc > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > >>> >>>>> > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> fscalc > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > >>> >>>>> > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> > > >>> >>>>> ##step6 create files of zeros for > > >>> group2 for each > > >>> >>>>> hemisphere > > >>> >>>>> fscalc > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> fscalc > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > >>> >>>>> > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> > > >>> >>>>> ##step7 create pvr files for group1 > > >>> for each hemisphere > > >>> >>>>> mri_concat > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > > >>> >>>>> lh.pvr_grp1_pet.nii.gz > > >>> >>>>> mri_concat > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > >>> >>>>> > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > > >>> >>>>> rh.pvr_grp1_pet.nii.gz > > >>> >>>>> > > >>> >>>>> ##step8 create pvr files for group2 > > >>> for each hemisphere > > >>> >>>>> mri_concat > > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> > allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > > >>> >>>>> lh.pvr_grp2_pet.nii.gz > > >>> >>>>> mri_concat > > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > >>> >>>>> > allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > > >>> >>>>> rh.pvr_grp2_pet.nii.gz > > >>> >>>>> > > >>> >>>>> ###-----repeat steps 1-8 for > cortical > > >>> thickness------- > > >>> >>>>> > > >>> >>>>> ###run glm-fit for group1 > > >>> >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz > > >>> --fsgd > > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > > >>> >>>>> lh_pvr_grp1_thickness.mgh --surf > fsaverage lh > > >>> --cortex > > >>> >>>>> --glmdir lh.grp1.pet.thickness.glmdir > > >>> >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz > > >>> --fsgd > > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > > >>> >>>>> rh_pvr_grp1_thickness.mgh --surf > fsaverage lh > > >>> --cortex > > >>> >>>>> --glmdir rh.grp1.pet.thickness.glmdir > > >>> >>>>> > > >>> >>>>> ###run glm-fit for group2 > > >>> >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz > > >>> --fsgd > > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > > >>> >>>>> lh_pvr_grp2_thickness.mgh --surf > fsaverage lh > > >>> --cortex > > >>> >>>>> --glmdir lh.grp2.pet.thickness.glmdir > > >>> >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz > > >>> --fsgd > > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > > >>> >>>>> rh_pvr_grp2_thickness.mgh --surf > fsaverage lh > > >>> --cortex > > >>> >>>>> --glmdir rh.grp2.pet.thickness.glmdir > > >>> >>>>> > > >>> >>>>> My questions. > > >>> >>>>> 1) will my fsgd file contain > > both groups? > > >>> >>>>> 2) If the answer from > question > > is yes, > > >>> i should have 2 > > >>> >>>>> contrasts (pvr1.mtx for group1 and > > >>> pvr2.mtx for > > >>> >>>>> group2). yes/no? > > >>> >>>>> 3) below is a sample of > my fsgd > > file. > > >>> are the > > >>> >>>>> constrasts correct? > > >>> >>>>> > > >>> >>>>> Thank you very much. > > >>> >>>>> Paul. > > >>> >>>>> The fsgd file lists: > > >>> >>>>> > > >>> > ------------------------------------------------------------- > > >>> >>>>> GroupDescriptorFile 1 > > >>> >>>>> Title Relationship Amy-thick reg out > > >>> age and education > > >>> >>>>> Class g1 > > >>> >>>>> Class g2 > > >>> >>>>> Variable Age Education > > >>> >>>>> Input XX1 g1 60 16 > > >>> >>>>> Input YY1 g2 62 20 > > >>> >>>>> > > >>> > ------------------------------------------------------------- > > >>> >>>>> matrix for group1: > > >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 > > >>> >>>>> is there a relationship > between > > >>> amyloid-thickness in group1 regressing > out age > > >>> >>>>> and education? > > >>> >>>>> matrix for group2: > > >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 > > >>> >>>>> is there a relationship > between > > >>> amyloid-thickness in group2 regressing > out age > > >>> >>>>> and education? > > >>> >>>>> > > >>> >>>>> On Thu, Aug 1, 2019 at > 9:44 PM > > Greve, > > >>> Douglas N.,Ph.D. > > >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > >>> >>>>> > > >>> >>>>> Each PVR adds a single column to > > >>> the design > > >>> >>>>> matrix. In a two group design, > > >>> this can make it > > >>> >>>>> tricky to set up. Let's say you > > >>> have 10 of group1 > > >>> >>>>> and 20 of group2. You will need to > > >>> create two PVR > > >>> >>>>> files, each with 30=10+20 frames. > > >>> In the first > > >>> >>>>> one, the first 10 frames will be > > >>> cortical > > >>> >>>>> thickness (or amyloid sampled on > > >>> the surface) of > > >>> >>>>> group1; the next 20 frames will be > > >>> all zeros. For > > >>> >>>>> the 2nd PVR, the first 10 frames > > >>> will be 0s and > > >>> >>>>> the next 20 frames will be the > > >>> cortical thickness > > >>> >>>>> (or amyloid) for group2. I would > > >>> start by running > > >>> >>>>> mris_preproc for the two groups > separate (so 2 > > >>> >>>>> files, one with 10 frames the > > >>> other 20 frames). > > >>> >>>>> Then create the file of zeros using > > >>> >>>>> fscalc group2.mgz mul 0 -o > > >>> group2.zeros.mgz > > >>> >>>>> Then > > >>> >>>>> mri_concat group1.mgz > group2.zeros.mgz --o > > pvr1.mgz > > >>> >>>>> Then create the contrast based on > > >>> the FSGD, but > > >>> >>>>> then add two more numbers, one for > > >>> PVR1 (which > > >>> >>>>> tests for the within group > > >>> correlation), and one > > >>> >>>>> for PVR2 > > >>> >>>>> > > >>> >>>>> > > >>> >>>>> On 8/1/2019 3:14 PM, miracle > > >>> ozzoude wrote: > > >>> >>>>>> > > >>> >>>>>> External Email - Use Caution > > >>> >>>>>> > > >>> >>>>>> Please, can anyone help me with > this. > > >>> >>>>>> Thank you > > >>> >>>>>> > > >>> >>>>>> Paul > > >>> >>>>>> > > >>> >>>>>> ---------- Forwarded message > --------- > > >>> >>>>>> From: *miracle ozzoude* > > >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>>> > > >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM > > >>> >>>>>> Subject: multimodal analysis > (pet and cortical > > >>> >>>>>> thickness relationship) using --pvr > > >>> >>>>>> To: Douglas N Greve > > >>> >>>>>> > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >>>>>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>> > > >>> >>>>>> > > >>> >>>>>> > > >>> >>>>>> Hello Experts, > > >>> >>>>>> > > >>> >>>>>> I am performing an analysis > > >>> looking at the > > >>> >>>>>> relationship between amyloid > uptake and > > cortical > > >>> >>>>>> thickness using --pvr flag in > mri_glmfit. > > I've 2 > > >>> >>>>>> groups and 2 variables (age and > education). I > > >>> >>>>>> want to run a within group > > >>> analysis while > > >>> >>>>>> regressing out age and education > (i.e. Within > > >>> >>>>>> group 1, is there a negative > > >>> relationship between > > >>> >>>>>> amyloid uptake and cortical > thickness > > regressing > > >>> >>>>>> out the effects of age and > > >>> education). > > >>> >>>>>> > > >>> >>>>>> However, i'm not sure how my pvr > contrasts > > will > > >>> >>>>>> look like. Below are my fsgd and > > >>> an attempt at > > >>> >>>>>> creating contrasts. Please, can > you let me > > know > > >>> >>>>>> if my contrasts are correct based > > >>> on my questions. > > >>> >>>>>> > > >>> >>>>>> Thank you. > > >>> >>>>>> > > >>> >>>>>> Best, > > >>> >>>>>> Paul > > >>> >>>>>> > > >>> >>>>>> The fsgd file lists: > > >>> >>>>>> > > >>> > ------------------------------------------------------------- > > >>> >>>>>> GroupDescriptorFile 1 > > >>> >>>>>> Title Relationship Amy-thick reg > > >>> out age and education > > >>> >>>>>> Class g1 > > >>> >>>>>> Class g2 > > >>> >>>>>> Variable Age Education > > >>> >>>>>> Input XX1 g1 60 16 > > >>> >>>>>> Input XX2 g1 58 14 > > >>> >>>>>> Input YY1 g2 62 20 > > >>> >>>>>> �� Input YY1 g2 62 20 > > >>> >>>>>> > > >>> > ------------------------------------------------------------- > > >>> >>>>>> matrix for group1: > > >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 > > >>> >>>>>> is there a relationship between > > >>> amyloid-thickness in group1 regressing > out age > > >>> >>>>>> and education? > > >>> >>>>>> matrix for group2: > > >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 > > >>> >>>>>> is there a relationship between > > >>> amyloid-thickness in group2 regressing > out age > > >>> >>>>>> and education? > > >>> >>>>>> > > >>> >>>>>> > > >>> >>>>>> > > >>> >>>>>> > > >>> >>>>>> > > _______________________________________________ > > >>> >>>>>> Freesurfer mailing list > > >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>>>> > > >>> >>>>> > _______________________________________________ > > >>> >>>>> Freesurfer mailing list > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >>>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>>>> > > >>> >>>>> > > >>> >>>>> > _______________________________________________ > > >>> >>>>> Freesurfer mailing list > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>>> > > >>> >>>> > _______________________________________________ > > >>> >>>> Freesurfer mailing list > > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>>> > > >>> >>>> > > >>> >>>> > _______________________________________________ > > >>> >>>> Freesurfer mailing list > > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >>> > > >>> >>> > > >>> >>> > _______________________________________________ > > >>> >>> Freesurfer mailing list > > >>> >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >> > > >>> >> > _______________________________________________ > > >>> >> Freesurfer mailing list > > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> >> > > >>> >> > > >>> >> > _______________________________________________ > > >>> >> Freesurfer mailing list > > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> >> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > > >>> > > _______________________________________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > >>> > > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > > >>> > > > >>> > > _______________________________________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > 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2:08 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
There are two ways, one easy, one hard. The easy way is to just use mri_vol2surf to sample on the surface, then compute the mean over any surface-based ROI that you want. The harder way is to create a new annotation, then run gtmseg again, then mri_gmptvc with the new gtmseg.
On 8/14/19 1:15 PM, miracle ozzoude wrote:
External Email - Use Caution
the surface based pet analysis in the petsurfer link use the whole brain. i want to do my surface base pet analysis on specific regions of the aparc not the entire regions. Should i use mri_vol2label to extract the covert the volume to labels, them mri_mergelabels to merge them? Thanks.
On Wed, Aug 14, 2019 at 1:08 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Then just do the standard PETsurfer processing On 8/14/19 12:59 PM, miracle ozzoude wrote: > > External Email - Use Caution > > I want to use the aparc ROI. something similar to doing ROI surface > base cortical thickness analysis where i used mri_annotation2label to > extract the regions and mri_mergelabels to merge them and run analysis > on them. > > On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Do you mean using different ROIs than in the aparc? If you want to > use > the aparc, then that is done in the standard processing. > > On 8/14/19 11:16 AM, miracle ozzoude wrote: > > > > External Email - Use Caution > > > > Hey Doug, > > > > If i want to do ROI surface base PET analysis using the method > on the > > PETsurfer website. Please, how do i go about doing it? I know there > > series of commands i will need to run before project it to the > surface > > using mri_vol2surf. > > thanks a lot > > best, > > Paul > > > > On Tue, Aug 13, 2019 at 11:00 AM miracle ozzoude > <miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> wrote: > > > > Awesome. thanks a lot for your help. I appreciate it. > > > > Best, > > Paul > > > > On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > You can use mri_surfcluster. That actually has an --fdr > flag, > > so you > > should not need to run mri_fdr. When you use --fdr, you > do not > > use > > --thmin. Use --sum to get the summary file > > > > On 8/13/19 10:50 AM, miracle ozzoude wrote: > > > > > > External Email - Use Caution > > > > > > Thanks a lot doug. I want to use mri_fdr instead of > > mri_glmfit-sim. > > > How do i get a summary of clusters like mri_glmfit-sim? I > > searched > > > through the forum and based on previous responses, The > > advice was to > > > do mri_fdr and then use mri_surfcluster without the fdr > > option to > > > obtain the summary of cluster. Is this correct? > > > Paul > > > > > > On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > > > > > > I don't know that there is much you can do. The > PVR is very > > > computationally intensive, and it does not surprise me > > that it is > > > taking > > > a long time. I don't think you need to do 10k > > permutations. I would > > > start with 1k. In the output, you will get a > confidence > > interval > > > for the > > > corrected p-value. This will shrink with the number of > > > permutations, but > > > if you're happy with it, no need to do more > > > > > > On 8/13/19 10:17 AM, miracle ozzoude wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Thanks Doug. My correction for multiple comparison > > using 10000 > > > > permutation and abs has been running for 3days. This > > is strange > > > > because i am using the --bg 10 and it usually takes > > 1hr to finish > > > > without the --pvr. how do i solve this? > > > > Below is my mri_glmfit and mri_glmfit-sim commands > > > > > > > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd > > dods --C $pvr1 > > > > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > > > > --pvr > ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf > > > fsaverage lh > > > > --cortex \ > > > > --glmdir ${wholebrain}/lh.pet.thickness.glmdir > --eres-save > > > > > > > > mri_glmfit-sim --glmdir > > ${wholebrain}/lh.pet.thickness.glmdir > > > --perm > > > > 10000 2 abs --perm-force --cwp 0.05 --2spaces > --bg 10 > > --overwrite > > > > > > > > > > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas > N.,Ph.D. > > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > wrote: > > > > > > > > You will have to click on the vertex you are > > interested in. The > > > > value will be -log10(pcorrected) where > pcorrected > > is the > > > corrected > > > > p-value > > > > > > > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: > > > >> > > > >> External Email - Use Caution > > > >> > > > >> these regions (please see below) came out > > significant for the > > > >> voxel-wise corrected map. I want to know their > > p-values. > > > >> mri-glmfit-sim doesn't give summary file for > > voxel-wise > > > corrected > > > >> map only for cluster-wise map. > > > >> image.png > > > >> > > > >> On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas > > N.,Ph.D. > > > >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > wrote: > > > >> > > > >> I'm not sure what you are looking for. The > > voxel-wise > > > >> analysis is voxel-wise, so there is no > > summary file for it > > > >> > > > >> On 8/12/2019 11:13 AM, miracle ozzoude > wrote: > > > >>> > > > >>> External Email - Use Caution > > > >>> > > > >>> Thanks Doug. Another question, how do > i find > > the p-values > > > >>> for voxel-wise map corrected for multiple > > comparisons at a > > > >>> voxel (rather than cluster) level > > > >>> (perm.th40.abs.sig.voxel.mgh). There is no > summary > > > file for it. > > > >>> Best, > > > >>> Paul > > > >>> > > > >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, > > Douglas N.,Ph.D. > > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > > >>> > > > >>> The 3 spaces is for left hemi, right > > hemi, and > > > >>> subcortical, so, if you > > > >>> are using all three then correct > for all 3 > > > >>> > > > >>> On 8/7/19 9:26 AM, miracle ozzoude > wrote: > > > >>> > > > > >>> > External Email - Use Caution > > > >>> > > > > >>> > Got it. Thanks a lot doug. If i have > > to correct for > > > >>> multiple > > > >>> > comparison in surface based pet > > analysis and > > > >>> mutlimodal analysis (pet > > > >>> > and thickness), should i use > --3spaces? > > > >>> > Thank you. > > > >>> > > > > >>> > best, > > > >>> > Paul > > > >>> > > > > >>> > On Mon, Aug 5, 2019 at 10:19 PM > Greve, > > Douglas > > > N.,Ph.D. > > > >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > >>> > > > > >>> > I think there is still something > > not right. You > > > >>> should just have > > > >>> > one mri_glmfit command for each > > hemisphere in > > > >>> which the input is > > > >>> > ?h.thickness.15.mgh, the > fsgdfile is > > > project.fsgd, > > > >>> you then > > > >>> > specify the pvrs for both groups > > (--pvr > > > >>> ?h.pvr_grp1_pet.nii.gz > > > >>> > --pvr ?h.pvr_grp2_pet.niigz) and > > then use that > > > >>> first contrast. The > > > >>> > second is the same as the first > > but with a > > > >>> reversed sign, but it > > > >>> > is not necessary since we always > > use unsigned > > > >>> tests and show both > > > >>> > signs (but you can still do it). > > > >>> > > > > >>> > On 8/5/2019 8:14 PM, miracle > > ozzoude wrote: > > > >>> >> > > > >>> >> External Email - Use > Caution > > > >>> >> > > > >>> >> I think i got it now. Something > > like this: > > > >>> >> > > > >>> >> ## group1 comes first in my > fsgd > > file. removing > > > >>> the effects of > > > >>> >> age and education > > > >>> >> ##amyloid-thickness. first pet > pvr = > > 1 for > > > group1 > > > >>> and 0 for group 2. > > > >>> >> mri_glmfit --y > > lh.thickness.15.mgh --fsgd > > > >>> project.fsgd dods --c > > > >>> >> pvr1.mtx --pvr > > lh.pvr_grp1_pet.nii.gz \ > > > >>> >> --pvr > > > >>> > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > >>> >> fsaverage lh --cortex --glmdir > > > >>> lh.pet.thickness.glmdir > > > >>> >> mri_glmfit --y > > rh.thickness.15.mgh --fsgd > > > >>> project.fsgd dods --c > > > >>> >> pvr1.mtx --pvr > > rh.pvr_grp1_pet.nii.gz \ > > > >>> >> --pvr > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > fsaverage > > > >>> >> lh --cortex --glmdir > > rh.pet.thickness.glmdir > > > >>> >> > > > >>> >> contrast = 0 0 0 0 0 0 1 -1 > > > >>> >> > > > >>> >> ##group 2 is second in my fsgd > file. > > > removing the > > > >>> effects of age > > > >>> >> and education > > > >>> >> ##amyloid-thickness. first pet > pvr = > > 0 for > > > group1 > > > >>> and 1 for group2 > > > >>> >> mri_glmfit --y > > lh.thickness.15.mgh --fsgd > > > >>> project.fsgd dods --c > > > >>> >> pvr2.mtx --pvr > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > >>> >> --pvr lh.pvr_grp2_pet.nii.gz > > -surf fsaverage lh > > > >>> --cortex --glmdir > > > >>> >> rh.pet.thickness.glmdir > > > >>> >> mri_glmfit --y > > rh.thickness.15.mgh --fsgd > > > >>> project.fsgd dods --c > > > >>> >> pvr2.mtx --pvr > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > >>> >> --pvr rh.pvr_grp2_pet.nii.gz > > -surf fsaverage lh > > > >>> --cortex --glmdir > > > >>> >> rh.pet.thickness.glmdir > > > >>> >> > > > >>> >> contrast = 0 0 0 0 0 0 -1 1 > > > >>> >> > > > >>> >> On Mon, Aug 5, 2019 at 6:47 PM > > Greve, Douglas > > > >>> N.,Ph.D. > > > >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > >>> >> > > > >>> >> It still looks like you are > > using a group > > > >>> specific input > > > >>> >> (--y). The input should be a > > simple > > > file with > > > >>> both groups > > > >>> >> (same input as you would use > > without pvr) > > > >>> >> > > > >>> >> On 8/5/2019 4:39 PM, > > miracooloz wrote: > > > >>> >>> > > > >>> >>> External Email - Use > Caution > > > >>> >>> > > > >>> >>> Thanks Doug. How about the > mri_glmfit > > > >>> commands? Since the > > > >>> >>> contrasts are correct, I > think the > > > commands > > > >>> should be right. > > > >>> >>> > > > >>> >>> Best, > > > >>> >>> Paul. > > > >>> >>> > > > >>> >>> > > > >>> >>> > > > >>> >>> Sent from my Samsung Galaxy > smartphone. > > > >>> >>> > > > >>> >>> -------- Original message > -------- > > > >>> >>> From: "Greve, Douglas N.,Ph.D." > > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > >>> >>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > >>> >>> Date: 2019-08-05 15:52 > (GMT-05:00) > > > >>> >>> To: > > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> >>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>> Subject: Re: [Freesurfer] Fwd: > > multimodal > > > >>> analysis (pet and > > > >>> >>> cortical thickness > relationship) using > > > --pvr > > > >>> >>> > > > >>> >>> Yes, that contrast is correct. > > > >>> >>> > > > >>> >>> On 8/5/2019 3:11 PM, miracle > > ozzoude > > > wrote: > > > >>> >>>> > > > >>> >>>> External Email - Use Caution > > > >>> >>>> > > > >>> >>>> Hello Doug, > > > >>> >>>> > > > >>> >>>> Thanks very much for your help. Your > > > >>> assumption was right > > > >>> >>>> in that i want to run a group > > comparison > > > >>> (i.e. test for a > > > >>> >>>> difference in amyloid-thickness slopes > > > >>> between the two > > > >>> >>>> groups). However, I am having a > > hard time > > > >>> creating the > > > >>> >>>> correct mri_glmfit and contrasts > > in this > > > >>> case. Based on > > > >>> >>>> your advice and searching through the > > > forum > > > >>> >>>> > > > >>> > > > > > > (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i > > > >>> >>>> need 2 PVRs for each hemisphere in the > > > >>> mri_glmfit command. > > > >>> >>>> I gave it another shot below. Please > > > let me > > > >>> know if i am > > > >>> >>>> correct. > > > >>> >>>> > > > >>> >>>> Thank you. > > > >>> >>>> Paul. > > > >>> >>>> > > > >>> >>>> ## group1 comes first in my fsgd file. > > > >>> removing the effects > > > >>> >>>> of age and education > > > >>> >>>> ##amyloid-thickness. first pet pvr > > = 1 for > > > >>> group1 and 0 for > > > >>> >>>> group 2. > > > >>> >>>> mri_glmfit --y > > > lh_pvr_grp1_thickness.mgh --fsgd > > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > > >>> lh.pvr_grp1_pet.nii.gz \ > > > >>> >>>> --pvr > > > >>> > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > >>> >>>> fsaverage lh --cortex --glmdir > > > >>> lh.pet.thickness.glmdir > > > >>> >>>> mri_glmfit --y > > > rh_pvr_grp1_thickness.mgh --fsgd > > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > > >>> rh.pvr_grp1_pet.nii.gz \ > > > >>> >>>> --pvr > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > >>> >>>> fsaverage lh --cortex --glmdir > > > >>> rh.pet.thickness.glmdir > > > >>> >>>> > > > >>> >>>> contrast = 0 0 0 0 0 0 1 -1 > > > >>> >>>> > > > >>> >>>> ##group 2 is second in my fsgd file. > > > >>> removing the effects > > > >>> >>>> of age and education > > > >>> >>>> ##amyloid-thickness. first pet pvr > > = 0 for > > > >>> group1 and 1 for > > > >>> >>>> group2 > > > >>> >>>> mri_glmfit --y > > > >>> lh_pvr_grp2_thickness.mgh --fsgd > > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > > >>> >>>> > > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf > > > >>> fsaverage lh --cortex > > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > > >>> >>>> mri_glmfit --y > > > rh_pvr_grp2_thickness.mgh --fsgd > > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > > >>> >>>> > > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf > > > >>> fsaverage lh --cortex > > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > > >>> >>>> > > > >>> >>>> contrast = 0 0 0 0 0 0 -1 1 > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, > > > >>> Douglas N.,Ph.D. > > > >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > >>> >>>> > > > >>> >>>> That mostly looks good. > > > >>> >>>> > > > >>> >>>> I would suggest is to change your > > > >>> smoothing command to > > > >>> >>>> something like > > > >>> >>>> mris_fwhm --smooth-only --s fsaverage > > > >>> --hemi lh --fwhm > > > >>> >>>> 5 --cortex --prune --i > > > >>> >>>> > > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > > >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>> The only difference will be > > that any > > > >>> vertices that are > > > >>> >>>> 0 in the input will be excluded > > > >>> (pruned) from the > > > >>> >>>> smoothing mask. > > > >>> >>>> > > > >>> >>>> The mri_glmfit command is not > > right. > > > >>> That command looks > > > >>> >>>> like it is for analyzing each > > group > > > >>> separately and > > > >>> >>>> independently. If that is what you > > want > > > >>> to do, then you > > > >>> >>>> don't need to go through all the > > > extra > > > >>> stuff of > > > >>> >>>> creating zero files, etc. I had > > > assumed > > > >>> that you wanted > > > >>> >>>> to do some kind of comparison > > between > > > >>> groups. If so, > > > >>> >>>> then you would use a single > > file with > > > >>> all your data in > > > >>> >>>> it (probably what you were using > > > >>> before), and your fsgd > > > >>> >>>> file would have both groups. > > > >>> >>>> > > > >>> >>>> 1) will my fsgd file contain both > > > groups? > > > >>> >>>> yes, see above > > > >>> >>>> 2) If the answer from question is > > > yes, > > > >>> i should have 2 > > > >>> >>>> contrasts (pvr1.mtx for group1 and > > > >>> pvr2.mtx for > > > >>> >>>> group2). yes/no? > > > >>> >>>> Again, if all you want to do is > > > to test > > > >>> the pvr for > > > >>> >>>> each group separately, then > > you don't > > > >>> need to go > > > >>> >>>> through the processes of creating > > > zero > > > >>> files, etc. In > > > >>> >>>> any event, if you want to test > > a pvr, > > > >>> then you need a > > > >>> >>>> contrast for it. > > > >>> >>>> 3) below is a sample of my > > fsgd file. > > > >>> are the > > > >>> >>>> constrasts correct? > > > >>> >>>> hard to say without resolving the > > > >>> questions above. You > > > >>> >>>> will need to have a value in the > > > >>> contrast for each pvr. > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> On 8/2/2019 3:56 PM, miracle > > > ozzoude wrote: > > > >>> >>>>> > > > >>> >>>>> External Email - Use Caution > > > >>> >>>>> > > > >>> >>>>> Hello Doug, > > > >>> >>>>> > > > >>> >>>>> Thanks for answering. Based on your > > > >>> explanation, i > > > >>> >>>>> wrote out a series of command needed > > > >>> to execute this. > > > >>> >>>>> Please let me know if i made any > > > >>> mistakes/correct. > > > >>> >>>>> ##step1 concatenating the 10 amyloid > > > >>> pet volumes files > > > >>> >>>>> projected to surface using > > > >>> mri_vol2surf for group1 > > > >>> >>>>> mri_concat --f grp1.lhmgxctx --o > > > >>> >>>>> > > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > > >>> >>>>> > > allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > > > >>> >>>>> > > > >>> >>>>> ##step2 concatenating the 20 amyloid > > > >>> pet volumes files > > > >>> >>>>> projected to surface using > > > >>> mri_vol2surf for group2 > > > >>> >>>>> mri_concat --f grp2.lhmgxctx --o > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > > >>> >>>>> > > allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > > > >>> >>>>> > > > >>> >>>>> ##step3 smooth on the surface for > > each > > > >>> hemisphere for > > > >>> >>>>> group1 > > > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > > > >>> --sval > > > >>> >>>>> > > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > > >>> >>>>> --cortex --tval > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > > > >>> --sval > > > >>> >>>>> > > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > > --fwhm 5 > > > >>> >>>>> --cortex --tval > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step4 smooth on the surface for > > each > > > >>> hemisphere for > > > >>> >>>>> group2 > > > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > > > >>> --sval > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > > >>> >>>>> --cortex --tval > > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > > > >>> --sval > > > >>> >>>>> > > allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz > > > --fwhm 5 > > > >>> >>>>> --cortex --tval > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step5 create files of zeros for > > > >>> group1 for each > > > >>> >>>>> hemisphere > > > >>> >>>>> fscalc > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > > >>> >>>>> > > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> fscalc > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > > >>> >>>>> > > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step6 create files of zeros for > > > >>> group2 for each > > > >>> >>>>> hemisphere > > > >>> >>>>> fscalc > > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> fscalc > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > > >>> >>>>> > > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step7 create pvr files for group1 > > > >>> for each hemisphere > > > >>> >>>>> mri_concat > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > > > >>> >>>>> lh.pvr_grp1_pet.nii.gz > > > >>> >>>>> mri_concat > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> > > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > > > >>> >>>>> rh.pvr_grp1_pet.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step8 create pvr files for group2 > > > >>> for each hemisphere > > > >>> >>>>> mri_concat > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > > > >>> >>>>> lh.pvr_grp2_pet.nii.gz > > > >>> >>>>> mri_concat > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> > > allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > > > >>> >>>>> rh.pvr_grp2_pet.nii.gz > > > >>> >>>>> > > > >>> >>>>> ###-----repeat steps 1-8 for > > cortical > > > >>> thickness------- > > > >>> >>>>> > > > >>> >>>>> ###run glm-fit for group1 > > > >>> >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz > > > >>> --fsgd > > > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > > > >>> >>>>> lh_pvr_grp1_thickness.mgh --surf > > fsaverage lh > > > >>> --cortex > > > >>> >>>>> --glmdir lh.grp1.pet.thickness.glmdir > > > >>> >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz > > > >>> --fsgd > > > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > > > >>> >>>>> rh_pvr_grp1_thickness.mgh --surf > > fsaverage lh > > > >>> --cortex > > > >>> >>>>> --glmdir rh.grp1.pet.thickness.glmdir > > > >>> >>>>> > > > >>> >>>>> ###run glm-fit for group2 > > > >>> >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz > > > >>> --fsgd > > > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > > > >>> >>>>> lh_pvr_grp2_thickness.mgh --surf > > fsaverage lh > > > >>> --cortex > > > >>> >>>>> --glmdir lh.grp2.pet.thickness.glmdir > > > >>> >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz > > > >>> --fsgd > > > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > > > >>> >>>>> rh_pvr_grp2_thickness.mgh --surf > > fsaverage lh > > > >>> --cortex > > > >>> >>>>> --glmdir rh.grp2.pet.thickness.glmdir > > > >>> >>>>> > > > >>> >>>>> My questions. > > > >>> >>>>> 1) will my fsgd file contain > > > both groups? > > > >>> >>>>> 2) If the answer from > > question > > > is yes, > > > >>> i should have 2 > > > >>> >>>>> contrasts (pvr1.mtx for group1 and > > > >>> pvr2.mtx for > > > >>> >>>>> group2). yes/no? > > > >>> >>>>> 3) below is a sample of > > my fsgd > > > file. > > > >>> are the > > > >>> >>>>> constrasts correct? > > > >>> >>>>> > > > >>> >>>>> Thank you very much. > > > >>> >>>>> Paul. > > > >>> >>>>> The fsgd file lists: > > > >>> >>>>> > > > >>> > > ------------------------------------------------------------- > > > >>> >>>>> GroupDescriptorFile 1 > > > >>> >>>>> Title Relationship Amy-thick reg out > > > >>> age and education > > > >>> >>>>> Class g1 > > > >>> >>>>> Class g2 > > > >>> >>>>> Variable Age Education > > > >>> >>>>> Input XX1 g1 60 16 > > > >>> >>>>> Input YY1 g2 62 20 > > > >>> >>>>> > > > >>> > > ------------------------------------------------------------- > > > >>> >>>>> matrix for group1: > > > >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 > > > >>> >>>>> is there a relationship > > between > > > >>> amyloid-thickness in group1 regressing > > out age > > > >>> >>>>> and education? > > > >>> >>>>> matrix for group2: > > > >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 > > > >>> >>>>> is there a relationship > > between > > > >>> amyloid-thickness in group2 regressing > > out age > > > >>> >>>>> and education? > > > >>> >>>>> > > > >>> >>>>> On Thu, Aug 1, 2019 at > > 9:44 PM > > > Greve, > > > >>> Douglas N.,Ph.D. > > > >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > >>> >>>>> > > > >>> >>>>> Each PVR adds a single column to > > > >>> the design > > > >>> >>>>> matrix. In a two group design, > > > >>> this can make it > > > >>> >>>>> tricky to set up. Let's say you > > > >>> have 10 of group1 > > > >>> >>>>> and 20 of group2. You will need to > > > >>> create two PVR > > > >>> >>>>> files, each with 30=10+20 frames. > > > >>> In the first > > > >>> >>>>> one, the first 10 frames will be > > > >>> cortical > > > >>> >>>>> thickness (or amyloid sampled on > > > >>> the surface) of > > > >>> >>>>> group1; the next 20 frames will be > > > >>> all zeros. For > > > >>> >>>>> the 2nd PVR, the first 10 frames > > > >>> will be 0s and > > > >>> >>>>> the next 20 frames will be the > > > >>> cortical thickness > > > >>> >>>>> (or amyloid) for group2. I would > > > >>> start by running > > > >>> >>>>> mris_preproc for the two groups > > separate (so 2 > > > >>> >>>>> files, one with 10 frames the > > > >>> other 20 frames). > > > >>> >>>>> Then create the file of zeros using > > > >>> >>>>> fscalc group2.mgz mul 0 -o > > > >>> group2.zeros.mgz > > > >>> >>>>> Then > > > >>> >>>>> mri_concat group1.mgz > > group2.zeros.mgz --o > > > pvr1.mgz > > > >>> >>>>> Then create the contrast based on > > > >>> the FSGD, but > > > >>> >>>>> then add two more numbers, one for > > > >>> PVR1 (which > > > >>> >>>>> tests for the within group > > > >>> correlation), and one > > > >>> >>>>> for PVR2 > > > >>> >>>>> > > > >>> >>>>> > > > >>> >>>>> On 8/1/2019 3:14 PM, miracle > > > >>> ozzoude wrote: > > > >>> >>>>>> > > > >>> >>>>>> External Email - Use Caution > > > >>> >>>>>> > > > >>> >>>>>> Please, can anyone help me with > > this. > > > >>> >>>>>> Thank you > > > >>> >>>>>> > > > >>> >>>>>> Paul > > > >>> >>>>>> > > > >>> >>>>>> ---------- Forwarded message > > --------- > > > >>> >>>>>> From: *miracle ozzoude* > > > >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> > > > >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>>>> > > > >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM > > > >>> >>>>>> Subject: multimodal analysis > > (pet and cortical > > > >>> >>>>>> thickness relationship) using --pvr > > > >>> >>>>>> To: Douglas N Greve > > > >>> >>>>>> > > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> >>>>>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> Hello Experts, > > > >>> >>>>>> > > > >>> >>>>>> I am performing an analysis > > > >>> looking at the > > > >>> >>>>>> relationship between amyloid > > uptake and > > > cortical > > > >>> >>>>>> thickness using --pvr flag in > > mri_glmfit. > > > I've 2 > > > >>> >>>>>> groups and 2 variables (age and > > education). I > > > >>> >>>>>> want to run a within group > > > >>> analysis while > > > >>> >>>>>> regressing out age and education > > (i.e. Within > > > >>> >>>>>> group 1, is there a negative > > > >>> relationship between > > > >>> >>>>>> amyloid uptake and cortical > > thickness > > > regressing > > > >>> >>>>>> out the effects of age and > > > >>> education). > > > >>> >>>>>> > > > >>> >>>>>> However, i'm not sure how my pvr > > contrasts > > > will > > > >>> >>>>>> look like. Below are my fsgd and > > > >>> an attempt at > > > >>> >>>>>> creating contrasts. Please, can > > you let me > > > know > > > >>> >>>>>> if my contrasts are correct based > > > >>> on my questions. > > > >>> >>>>>> > > > >>> >>>>>> Thank you. > > > >>> >>>>>> > > > >>> >>>>>> Best, > > > >>> >>>>>> Paul > > > >>> >>>>>> > > > >>> >>>>>> The fsgd file lists: > > > >>> >>>>>> > > > >>> > > ------------------------------------------------------------- > > > >>> >>>>>> GroupDescriptorFile 1 > > > >>> >>>>>> Title Relationship Amy-thick reg > > > >>> out age and education > > > >>> >>>>>> Class g1 > > > >>> >>>>>> Class g2 > > > >>> >>>>>> Variable Age Education > > > >>> >>>>>> Input XX1 g1 60 16 > > > >>> >>>>>> Input XX2 g1 58 14 > > > >>> >>>>>> Input YY1 g2 62 20 > > > >>> >>>>>> �� Input YY1 g2 62 20 > > > >>> >>>>>> > > > >>> > > ------------------------------------------------------------- > > > >>> >>>>>> matrix for group1: > > > >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 > > > >>> >>>>>> is there a relationship between > > > >>> amyloid-thickness in group1 regressing > > out age > > > >>> >>>>>> and education? > > > >>> >>>>>> matrix for group2: > > > >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 > > > >>> >>>>>> is there a relationship between > > > >>> amyloid-thickness in group2 regressing > > out age > > > >>> >>>>>> and education? > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > _______________________________________________ > > > >>> >>>>>> Freesurfer mailing list > > > >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>>>> > > > >>> >>>>> > > _______________________________________________ > > > >>> >>>>> Freesurfer mailing list > > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> >>>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>>>> > > > >>> >>>>> > > > >>> >>>>> > > _______________________________________________ > > > >>> >>>>> Freesurfer mailing list > > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>>> > > > >>> >>>> > > _______________________________________________ > > > >>> >>>> Freesurfer mailing list > > > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> >>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > 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<mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> > > _______________________________________________ > > > >>> >>>> Freesurfer mailing list > > > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu 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<mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >> > > > >>> >> > > > >>> >> > > _______________________________________________ > > > >>> >> Freesurfer mailing list > > > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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<mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> > > > > >>> > > > _______________________________________________ > > > >>> > Freesurfer mailing list > > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu 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<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu 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2:29 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
External Email - Use Caution
I will go the easy way. By 'compute mean" do you mean, using mri_annotation2label to get the label files, merge them using mri_mergelabels to them, smooth using mris_fwhm with --label , and run mri_glmfit with the --label. I tried something similar because the pet volumes are already in the surf. mri_vol2surf --mov $in_dir/${session}.gtmpvc.output/mgx.ctxgm.nii.gz --reg $in_dir/${session}.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 \ --o $in_dir/lh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage mri_vol2surf --mov $in_dir/${session}.gtmpvc.output/mgx.ctxgm.nii.gz --reg $in_dir/${session}.gtmpvc.output/aux/bbpet2anat.lta --hemi rh --projfrac 0.5 \ --o $in_dir/rh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage
##extract labels from fsaverage mri_annotation2label --subject fsaverage --hemi lh --outdir ${SUBJECTS_DIR}/fsaverage/label mri_annotation2label --subject fsaverage --hemi rh --outdir ${SUBJECTS_DIR}/fsaverage/label
# #merge the ROI to form global ROI. e.g frontal lobe # #right hemisphere mri_mergelabels -i ${SUBJECTS_DIR}/fsaverage/label/rh.precuneus.label -i ${SUBJECTS_DIR}/fsaverage/label/rh.posteriorcingulate.label \ -i ${SUBJECTS_DIR}/fsaverage/label/rh.isthmuscingulate.label -i ${SUBJECTS_DIR}/fsaverage/label/rh.insula.label \ -i ${SUBJECTS_DIR}/fsaverage/label/rh.medialorbitofrontal.label -i ${SUBJECTS_DIR}/fsaverage/label/rh.lateralorbitofrontal.label \ -o ${SUBJECTS_DIR}/fsaverage/label/rh.early.label # ##left hemisphere mri_mergelabels -i ${SUBJECTS_DIR}/fsaverage/label/lh.precuneus.label -i ${SUBJECTS_DIR}/fsaverage/label/lh.posteriorcingulate.label \ -i ${SUBJECTS_DIR}/fsaverage/label/lh.isthmuscingulate.label -i ${SUBJECTS_DIR}/fsaverage/label/lh.insula.label \ -i ${SUBJECTS_DIR}/fsaverage/label/lh.medialorbitofrontal.label -i ${SUBJECTS_DIR}/fsaverage/label/lh.lateralorbitofrontal.label \ -o ${SUBJECTS_DIR}/fsaverage/label/lh.early.label
# # # #concatenate all subjects mri_concat --f "$lhmgxctxgm" --o ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune mri_concat --f "$rhmgxctxgm" --o ${results_dir}/all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune
# # # # #smooth on the surface mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --prune --label ${SUBJECTS_DIR}/fsaverage/label/lh.early.label \ --i ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --o ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz mris_fwhm --smooth-only --s fsaverage --hemi rh --fwhm 5 --prune --label ${SUBJECTS_DIR}/fsaverage/label/rh.early.label \ --i ${results_dir}/all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --o ${results_dir}/all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz
# # # # # Run GLM analysis mri_glmfit --y ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --fsgd $Pet_fsgd dods --C $martrix1 \ --surf fsaverage lh --label ${SUBJECTS_DIR}/fsaverage/label/lh.early.label --glmdir ${results_dir}/lh.pet.1.$Pet_fsgd.glmdir mri_glmfit --y ${results_dir}/all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz --fsgd $Pet_fsgd dods --C $martrix1 \ --surf fsaverage rh --label ${SUBJECTS_DIR}/fsaverage/label/rh.early.label --glmdir ${results_dir}/rh.pet.1.$Pet_fsgd.glmdir
On Wed, Aug 14, 2019 at 2:09 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
There are two ways, one easy, one hard. The easy way is to just use mri_vol2surf to sample on the surface, then compute the mean over any surface-based ROI that you want. The harder way is to create a new annotation, then run gtmseg again, then mri_gmptvc with the new gtmseg.
On 8/14/19 1:15 PM, miracle ozzoude wrote:
External Email - Use Cautionthe surface based pet analysis in the petsurfer link use the whole brain. i want to do my surface base pet analysis on specific regions of the aparc not the entire regions. Should i use mri_vol2label to extract the covert the volume to labels, them mri_mergelabels to merge them? Thanks.
On Wed, Aug 14, 2019 at 1:08 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Then just do the standard PETsurfer processing On 8/14/19 12:59 PM, miracle ozzoude wrote: > > External Email - Use Caution > > I want to use the aparc ROI. something similar to doing ROI surface > base cortical thickness analysis where i used mri_annotation2label to > extract the regions and mri_mergelabels to merge them and run analysis > on them. > > On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Do you mean using different ROIs than in the aparc? If you want to > use > the aparc, then that is done in the standard processing. > > On 8/14/19 11:16 AM, miracle ozzoude wrote: > > > > External Email - Use Caution > > > > Hey Doug, > > > > If i want to do ROI surface base PET analysis using themethod
> on the > > PETsurfer website. Please, how do i go about doing it? I know there > > series of commands i will need to run before project it tothe
> surface > > using mri_vol2surf. > > thanks a lot > > best, > > Paul > > > > On Tue, Aug 13, 2019 at 11:00 AM miracle ozzoude > <miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> wrote: > > > > Awesome. thanks a lot for your help. I appreciate it. > > > > Best, > > Paul > > > > On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > You can use mri_surfcluster. That actually has an --fdr > flag, > > so you > > should not need to run mri_fdr. When you use --fdr, you > do not > > use > > --thmin. Use --sum to get the summary file > > > > On 8/13/19 10:50 AM, miracle ozzoude wrote: > > > > > > External Email - Use Caution > > > > > > Thanks a lot doug. I want to use mri_fdr instead of > > mri_glmfit-sim. > > > How do i get a summary of clusters like mri_glmfit-sim? I > > searched > > > through the forum and based on previous responses, The > > advice was to > > > do mri_fdr and then use mri_surfcluster without the fdr > > option to > > > obtain the summary of cluster. Is this correct? > > > Paul > > > > > > On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D. > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> wrote: > > > > > > I don't know that there is much you can do. The > PVR is very > > > computationally intensive, and it does not surprise me > > that it is > > > taking > > > a long time. I don't think you need to do 10k > > permutations. I would > > > start with 1k. In the output, you will get a > confidence > > interval > > > for the > > > corrected p-value. This will shrink with the number of > > > permutations, but > > > if you're happy with it, no need to do more > > > > > > On 8/13/19 10:17 AM, miracle ozzoude wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Thanks Doug. My correction for multiple comparison > > using 10000 > > > > permutation and abs has been running for 3days. This > > is strange > > > > because i am using the --bg 10 and it usually takes > > 1hr to finish > > > > without the --pvr. how do i solve this? > > > > Below is my mri_glmfit and mri_glmfit-sim commands > > > > > > > > mri_glmfit --y ${lhpetsurfimg} --fsgd $bothgrpfsgd > > dods --C $pvr1 > > > > --pvr ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > > > > --pvr > ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf > > > fsaverage lh > > > > --cortex \ > > > > --glmdir${wholebrain}/lh.pet.thickness.glmdir
> --eres-save > > > > > > > > mri_glmfit-sim --glmdir > > ${wholebrain}/lh.pet.thickness.glmdir > > > --perm > > > > 10000 2 abs --perm-force --cwp 0.05 --2spaces > --bg 10 > > --overwrite > > > > > > > > > > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas > N.,Ph.D. > > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > wrote: > > > > > > > > You will have to click on the vertex you are > > interested in. The > > > > value will be -log10(pcorrected) where > pcorrected > > is the > > > corrected > > > > p-value > > > > > > > > On 8/12/2019 11:24 AM, miracle ozzoude wrote: > > > >> > > > >> External Email - Use Caution > > > >> > > > >> these regions (please see below) cameout
> > significant for the > > > >> voxel-wise corrected map. I want to know their > > p-values. > > > >> mri-glmfit-sim doesn't give summary file for > > voxel-wise > > > corrected > > > >> map only for cluster-wise map. > > > >> image.png > > > >> > > > >> On Mon, Aug 12, 2019 at 11:19 AM Greve, Douglas > > N.,Ph.D. > > > >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > wrote: > > > >> > > > >> I'm not sure what you are looking for. The > > voxel-wise > > > >> analysis is voxel-wise, so there is no > > summary file for it > > > >> > > > >> On 8/12/2019 11:13 AM, miracle ozzoude > wrote: > > > >>> > > > >>> External Email - Use Caution > > > >>> > > > >>> Thanks Doug. Another question, how do > i find > > the p-values > > > >>> for voxel-wise map corrected for multiple > > comparisons at a > > > >>> voxel (rather than cluster) level > > > >>> (perm.th40.abs.sig.voxel.mgh). There is no > summary > > > file for it. > > > >>> Best, > > > >>> Paul > > > >>> > > > >>> On Wed, Aug 7, 2019 at 11:08 AM Greve, > > Douglas N.,Ph.D. > > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > > >>> > > > >>> The 3 spaces is for left hemi, right > > hemi, and > > > >>> subcortical, so, if you > > > >>> are using all three thencorrect
> for all 3 > > > >>> > > > >>> On 8/7/19 9:26 AM, miracle ozzoude > wrote: > > > >>> > > > > >>> > External Email - Use Caution > > > >>> > > > > >>> > Got it. Thanks a lot doug. If i have > > to correct for > > > >>> multiple > > > >>> > comparison in surface based pet > > analysis and > > > >>> mutlimodal analysis (pet > > > >>> > and thickness), should i use > --3spaces? > > > >>> > Thank you. > > > >>> > > > > >>> > best, > > > >>> > Paul > > > >>> > > > > >>> > On Mon, Aug 5, 2019 at 10:19 PM > Greve, > > Douglas > > > N.,Ph.D. > > > >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > >>> > > > > >>> > I think there is still something > > not right. You > > > >>> should just have > > > >>> > one mri_glmfit command for each > > hemisphere in > > > >>> which the input is > > > >>> > ?h.thickness.15.mgh, the > fsgdfile is > > > project.fsgd, > > > >>> you then > > > >>> > specify the pvrs for both groups > > (--pvr > > > >>> ?h.pvr_grp1_pet.nii.gz > > > >>> > --pvr ?h.pvr_grp2_pet.niigz) and > > then use that > > > >>> first contrast. The > > > >>> > second is the same as the first > > but with a > > > >>> reversed sign, but it > > > >>> > is not necessary since we always > > use unsigned > > > >>> tests and show both > > > >>> > signs (but you can still do it). > > > >>> > > > > >>> > On 8/5/2019 8:14 PM, miracle > > ozzoude wrote: > > > >>> >> > > > >>> >> External Email - Use > Caution > > > >>> >> > > > >>> >> I think i got it now. Something > > like this: > > > >>> >> > > > >>> >> ## group1 comes first in my > fsgd > > file. removing > > > >>> the effects of > > > >>> >> age and education > > > >>> >> ##amyloid-thickness. first pet > pvr = > > 1 for > > > group1 > > > >>> and 0 for group 2. > > > >>> >> mri_glmfit --y > > lh.thickness.15.mgh --fsgd > > > >>> project.fsgd dods --c > > > >>> >> pvr1.mtx --pvr > > lh.pvr_grp1_pet.nii.gz \ > > > >>> >> --pvr > > > >>> > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > >>> >> fsaverage lh --cortex --glmdir > > > >>> lh.pet.thickness.glmdir > > > >>> >> mri_glmfit --y > > rh.thickness.15.mgh --fsgd > > > >>> project.fsgd dods --c > > > >>> >> pvr1.mtx --pvr > > rh.pvr_grp1_pet.nii.gz \ > > > >>> >> --pvr > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > fsaverage > > > >>> >> lh --cortex --glmdir > > rh.pet.thickness.glmdir > > > >>> >> > > > >>> >> contrast = 0 0 0 0 0 0 1 -1 > > > >>> >> > > > >>> >> ##group 2 is second in my fsgd > file. > > > removing the > > > >>> effects of age > > > >>> >> and education > > > >>> >> ##amyloid-thickness. first pet > pvr = > > 0 for > > > group1 > > > >>> and 1 for group2 > > > >>> >> mri_glmfit --y > > lh.thickness.15.mgh --fsgd > > > >>> project.fsgd dods --c > > > >>> >> pvr2.mtx --pvr > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > >>> >> --pvr lh.pvr_grp2_pet.nii.gz > > -surf fsaverage lh > > > >>> --cortex --glmdir > > > >>> >> rh.pet.thickness.glmdir > > > >>> >> mri_glmfit --y > > rh.thickness.15.mgh --fsgd > > > >>> project.fsgd dods --c > > > >>> >> pvr2.mtx --pvr > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > >>> >> --pvr rh.pvr_grp2_pet.nii.gz > > -surf fsaverage lh > > > >>> --cortex --glmdir > > > >>> >> rh.pet.thickness.glmdir > > > >>> >> > > > >>> >> contrast = 0 0 0 0 0 0 -1 1 > > > >>> >> > > > >>> >> On Mon, Aug 5, 2019 at 6:47 PM > > Greve, Douglas > > > >>> N.,Ph.D. > > > >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > >>> >> > > > >>> >> It still looks like you are > > using a group > > > >>> specific input > > > >>> >> (--y). The input should be a > > simple > > > file with > > > >>> both groups > > > >>> >> (same input as you would use > > without pvr) > > > >>> >> > > > >>> >> On 8/5/2019 4:39 PM, > > miracooloz wrote: > > > >>> >>> > > > >>> >>> External Email - Use > Caution > > > >>> >>> > > > >>> >>> Thanks Doug. How about the > mri_glmfit > > > >>> commands? Since the > > > >>> >>> contrasts are correct, I > think the > > > commands > > > >>> should be right. > > > >>> >>> > > > >>> >>> Best, > > > >>> >>> Paul. > > > >>> >>> > > > >>> >>> > > > >>> >>> > > > >>> >>> Sent from my Samsung Galaxy > smartphone. > > > >>> >>> > > > >>> >>> -------- Original message > -------- > > > >>> >>> From: "Greve, Douglas N.,Ph.D." > > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > >>> >>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > >>> >>> Date: 2019-08-05 15:52 > (GMT-05:00) > > > >>> >>> To: > > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> >>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>> Subject: Re: [Freesurfer] Fwd: > > multimodal > > > >>> analysis (pet and > > > >>> >>> cortical thickness > relationship) using > > > --pvr > > > >>> >>> > > > >>> >>> Yes, that contrast is correct. > > > >>> >>> > > > >>> >>> On 8/5/2019 3:11 PM, miracle > > ozzoude > > > wrote: > > > >>> >>>> > > > >>> >>>> External Email - Use Caution > > > >>> >>>> > > > >>> >>>> Hello Doug, > > > >>> >>>> > > > >>> >>>> Thanks very much for your help. Your > > > >>> assumption was right > > > >>> >>>> in that i want to run a group > > comparison > > > >>> (i.e. test for a > > > >>> >>>> difference in amyloid-thickness slopes > > > >>> between the two > > > >>> >>>> groups). However, I am having a > > hard time > > > >>> creating the > > > >>> >>>> correct mri_glmfit and contrasts > > in this > > > >>> case. Based on > > > >>> >>>> your advice and searching throughthe
> > > forum > > > >>> >>>> > > > >>> > > > > > > (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.ht... ), i
> > > >>> >>>> need 2 PVRs for each hemisphere in the > > > >>> mri_glmfit command. > > > >>> >>>> I gave it another shot below. Please > > > let me > > > >>> know if i am > > > >>> >>>> correct. > > > >>> >>>> > > > >>> >>>> Thank you. > > > >>> >>>> Paul. > > > >>> >>>> > > > >>> >>>> ## group1 comes first in my fsgd file. > > > >>> removing the effects > > > >>> >>>> of age and education > > > >>> >>>> ##amyloid-thickness. first pet pvr > > = 1 for > > > >>> group1 and 0 for > > > >>> >>>> group 2. > > > >>> >>>> mri_glmfit --y > > > lh_pvr_grp1_thickness.mgh --fsgd > > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > > >>> lh.pvr_grp1_pet.nii.gz \ > > > >>> >>>> --pvr > > > >>> > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > >>> >>>> fsaverage lh --cortex --glmdir > > > >>> lh.pet.thickness.glmdir > > > >>> >>>> mri_glmfit --y > > > rh_pvr_grp1_thickness.mgh --fsgd > > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > > >>> rh.pvr_grp1_pet.nii.gz \ > > > >>> >>>> --pvr > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > >>> >>>> fsaverage lh --cortex --glmdir > > > >>> rh.pet.thickness.glmdir > > > >>> >>>> > > > >>> >>>> contrast = 0 0 0 0 0 0 1 -1 > > > >>> >>>> > > > >>> >>>> ##group 2 is second in my fsgd file. > > > >>> removing the effects > > > >>> >>>> of age and education > > > >>> >>>> ##amyloid-thickness. first pet pvr > > = 0 for > > > >>> group1 and 1 for > > > >>> >>>> group2 > > > >>> >>>> mri_glmfit --y > > > >>> lh_pvr_grp2_thickness.mgh --fsgd > > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > > >>> >>>> > > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf > > > >>> fsaverage lh --cortex > > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > > >>> >>>> mri_glmfit --y > > > rh_pvr_grp2_thickness.mgh --fsgd > > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > > >>> >>>> > > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf > > > >>> fsaverage lh --cortex > > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > > >>> >>>> > > > >>> >>>> contrast = 0 0 0 0 0 0 -1 1 > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, > > > >>> Douglas N.,Ph.D. > > > >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > >>> >>>> > > > >>> >>>> That mostly looks good. > > > >>> >>>> > > > >>> >>>> I would suggest is to changeyour
> > > >>> smoothing command to > > > >>> >>>> something like > > > >>> >>>> mris_fwhm --smooth-only --sfsaverage
> > > >>> --hemi lh --fwhm > > > >>> >>>> 5 --cortex --prune --i > > > >>> >>>> > > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > > >>> >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>> The only difference will be > > that any > > > >>> vertices that are > > > >>> >>>> 0 in the input will be excluded > > > >>> (pruned) from the > > > >>> >>>> smoothing mask. > > > >>> >>>> > > > >>> >>>> The mri_glmfit command is not > > right. > > > >>> That command looks > > > >>> >>>> like it is for analyzing each > > group > > > >>> separately and > > > >>> >>>> independently. If that is what you > > want > > > >>> to do, then you > > > >>> >>>> don't need to go through all the > > > extra > > > >>> stuff of > > > >>> >>>> creating zero files, etc. I had > > > assumed > > > >>> that you wanted > > > >>> >>>> to do some kind of comparison > > between > > > >>> groups. If so, > > > >>> >>>> then you would use a single > > file with > > > >>> all your data in > > > >>> >>>> it (probably what you were using > > > >>> before), and your fsgd > > > >>> >>>> file would have both groups. > > > >>> >>>> > > > >>> >>>> 1) will my fsgd file containboth
> > > groups? > > > >>> >>>> yes, see above > > > >>> >>>> 2) If the answer from questionis
> > > yes, > > > >>> i should have 2 > > > >>> >>>> contrasts (pvr1.mtx for group1 and > > > >>> pvr2.mtx for > > > >>> >>>> group2). yes/no? > > > >>> >>>> Again, if all you want to do is > > > to test > > > >>> the pvr for > > > >>> >>>> each group separately, then > > you don't > > > >>> need to go > > > >>> >>>> through the processes ofcreating
> > > zero > > > >>> files, etc. In > > > >>> >>>> any event, if you want to test > > a pvr, > > > >>> then you need a > > > >>> >>>> contrast for it. > > > >>> >>>> 3) below is a sample of my > > fsgd file. > > > >>> are the > > > >>> >>>> constrasts correct? > > > >>> >>>> hard to say without resolvingthe
> > > >>> questions above. You > > > >>> >>>> will need to have a value in the > > > >>> contrast for each pvr. > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> On 8/2/2019 3:56 PM, miracle > > > ozzoude wrote: > > > >>> >>>>> > > > >>> >>>>> External Email - UseCaution
> > > >>> >>>>> > > > >>> >>>>> Hello Doug, > > > >>> >>>>> > > > >>> >>>>> Thanks for answering. Based on your > > > >>> explanation, i > > > >>> >>>>> wrote out a series of commandneeded
> > > >>> to execute this. > > > >>> >>>>> Please let me know if i made any > > > >>> mistakes/correct. > > > >>> >>>>> ##step1 concatenating the 10amyloid
> > > >>> pet volumes files > > > >>> >>>>> projected to surface using > > > >>> mri_vol2surf for group1 > > > >>> >>>>> mri_concat --f grp1.lhmgxctx --o > > > >>> >>>>> > > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > > >>> >>>>> > > allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > > > >>> >>>>> > > > >>> >>>>> ##step2 concatenating the 20amyloid
> > > >>> pet volumes files > > > >>> >>>>> projected to surface using > > > >>> mri_vol2surf for group2 > > > >>> >>>>> mri_concat --f grp2.lhmgxctx --o > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > > >>> >>>>> > > allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > > > >>> >>>>> > > > >>> >>>>> ##step3 smooth on the surface for > > each > > > >>> hemisphere for > > > >>> >>>>> group1 > > > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > > > >>> --sval > > > >>> >>>>> > > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > > >>> >>>>> --cortex --tval > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > > > >>> --sval > > > >>> >>>>> > > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > > --fwhm 5 > > > >>> >>>>> --cortex --tval > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step4 smooth on the surface for > > each > > > >>> hemisphere for > > > >>> >>>>> group2 > > > >>> >>>>> mri_surf2surf --hemi lh --s fsaverage > > > >>> --sval > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > > >>> >>>>> --cortex --tval > > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> mri_surf2surf --hemi rh --s fsaverage > > > >>> --sval > > > >>> >>>>> > > allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz > > > --fwhm 5 > > > >>> >>>>> --cortex --tval > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step5 create files of zeros for > > > >>> group1 for each > > > >>> >>>>> hemisphere > > > >>> >>>>> fscalc > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > > >>> >>>>> > > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> fscalc > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > > >>> >>>>> > > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step6 create files of zeros for > > > >>> group2 for each > > > >>> >>>>> hemisphere > > > >>> >>>>> fscalc > > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> fscalc > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > > > >>> >>>>> > > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step7 create pvr files for group1 > > > >>> for each hemisphere > > > >>> >>>>> mri_concat > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > > > >>> >>>>> lh.pvr_grp1_pet.nii.gz > > > >>> >>>>> mri_concat > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > > >>> >>>>> > > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > > > >>> >>>>> rh.pvr_grp1_pet.nii.gz > > > >>> >>>>> > > > >>> >>>>> ##step8 create pvr files for group2 > > > >>> for each hemisphere > > > >>> >>>>> mri_concat > > > >>>allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz
> > > >>> >>>>> > > allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > > > >>> >>>>> lh.pvr_grp2_pet.nii.gz > > > >>> >>>>> mri_concat > > > >>>allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz
> > > >>> >>>>> > > allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > > > >>> >>>>> rh.pvr_grp2_pet.nii.gz > > > >>> >>>>> > > > >>> >>>>> ###-----repeat steps 1-8 for > > cortical > > > >>> thickness------- > > > >>> >>>>> > > > >>> >>>>> ###run glm-fit for group1 > > > >>> >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz > > > >>> --fsgd > > > >>> >>>>> project.fsgd dods --c pvr1.mtx--pvr
> > > >>> >>>>> lh_pvr_grp1_thickness.mgh --surf > > fsaverage lh > > > >>> --cortex > > > >>> >>>>> --glmdir lh.grp1.pet.thickness.glmdir > > > >>> >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz > > > >>> --fsgd > > > >>> >>>>> project.fsgd dods --c pvr1.mtx--pvr
> > > >>> >>>>> rh_pvr_grp1_thickness.mgh --surf > > fsaverage lh > > > >>> --cortex > > > >>> >>>>> --glmdir rh.grp1.pet.thickness.glmdir > > > >>> >>>>> > > > >>> >>>>> ###run glm-fit for group2 > > > >>> >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz > > > >>> --fsgd > > > >>> >>>>> project.fsgd dods --c pvr2.mtx--pvr
> > > >>> >>>>> lh_pvr_grp2_thickness.mgh --surf > > fsaverage lh > > > >>> --cortex > > > >>> >>>>> --glmdir lh.grp2.pet.thickness.glmdir > > > >>> >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz > > > >>> --fsgd > > > >>> >>>>> project.fsgd dods --c pvr2.mtx--pvr
> > > >>> >>>>> rh_pvr_grp2_thickness.mgh --surf > > fsaverage lh > > > >>> --cortex > > > >>> >>>>> --glmdir rh.grp2.pet.thickness.glmdir > > > >>> >>>>> > > > >>> >>>>> My questions. > > > >>> >>>>> 1) will my fsgd filecontain
> > > both groups? > > > >>> >>>>> 2) If the answer from > > question > > > is yes, > > > >>> i should have 2 > > > >>> >>>>> contrasts (pvr1.mtx for group1 and > > > >>> pvr2.mtx for > > > >>> >>>>> group2). yes/no? > > > >>> >>>>> 3) below is a sample of > > my fsgd > > > file. > > > >>> are the > > > >>> >>>>> constrasts correct? > > > >>> >>>>> > > > >>> >>>>> Thank you very much. > > > >>> >>>>> Paul. > > > >>> >>>>> The fsgd file lists: > > > >>> >>>>> > > > >>> > > ------------------------------------------------------------- > > > >>> >>>>> GroupDescriptorFile 1 > > > >>> >>>>> Title Relationship Amy-thick regout
> > > >>> age and education > > > >>> >>>>> Class g1 > > > >>> >>>>> Class g2 > > > >>> >>>>> Variable Age Education > > > >>> >>>>> Input XX1 g1 60 16 > > > >>> >>>>> Input YY1 g2 62 20 > > > >>> >>>>> > > > >>> > > ------------------------------------------------------------- > > > >>> >>>>> matrix for group1: > > > >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 > > > >>> >>>>> is there a relationship > > between > > > >>> amyloid-thickness in group1 regressing > > out age > > > >>> >>>>> and education? > > > >>> >>>>> matrix for group2: > > > >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 > > > >>> >>>>> is there a relationship > > between > > > >>> amyloid-thickness in group2 regressing > > out age > > > >>> >>>>> and education? > > > >>> >>>>> > > > >>> >>>>> On Thu, Aug 1, 2019 at > > 9:44 PM > > > Greve, > > > >>> Douglas N.,Ph.D. > > > >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > >>> >>>>> > > > >>> >>>>> Each PVR adds a single column to > > > >>> the design > > > >>> >>>>> matrix. In a two group design, > > > >>> this can make it > > > >>> >>>>> tricky to set up. Let's say you > > > >>> have 10 of group1 > > > >>> >>>>> and 20 of group2. You will need to > > > >>> create two PVR > > > >>> >>>>> files, each with 30=10+20 frames. > > > >>> In the first > > > >>> >>>>> one, the first 10 frames will be > > > >>> cortical > > > >>> >>>>> thickness (or amyloid sampled on > > > >>> the surface) of > > > >>> >>>>> group1; the next 20 frames will be > > > >>> all zeros. For > > > >>> >>>>> the 2nd PVR, the first 10 frames > > > >>> will be 0s and > > > >>> >>>>> the next 20 frames will be the > > > >>> cortical thickness > > > >>> >>>>> (or amyloid) for group2. I would > > > >>> start by running > > > >>> >>>>> mris_preproc for the two groups > > separate (so 2 > > > >>> >>>>> files, one with 10 frames the > > > >>> other 20 frames). > > > >>> >>>>> Then create the file of zeros using > > > >>> >>>>> fscalc group2.mgz mul 0 -o > > > >>> group2.zeros.mgz > > > >>> >>>>> Then > > > >>> >>>>> mri_concat group1.mgz > > group2.zeros.mgz --o > > > pvr1.mgz > > > >>> >>>>> Then create the contrast based on > > > >>> the FSGD, but > > > >>> >>>>> then add two more numbers, one for > > > >>> PVR1 (which > > > >>> >>>>> tests for the within group > > > >>> correlation), and one > > > >>> >>>>> for PVR2 > > > >>> >>>>> > > > >>> >>>>> > > > >>> >>>>> On 8/1/2019 3:14 PM, miracle > > > >>> ozzoude wrote: > > > >>> >>>>>> > > > >>> >>>>>> External Email - Use Caution > > > >>> >>>>>> > > > >>> >>>>>> Please, can anyone help me with > > this. > > > >>> >>>>>> Thank you > > > >>> >>>>>> > > > >>> >>>>>> Paul > > > >>> >>>>>> > > > >>> >>>>>> ---------- Forwarded message > > --------- > > > >>> >>>>>> From: *miracle ozzoude* > > > >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> > > > >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>
> > > >>> >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM > > > >>> >>>>>> Subject: multimodal analysis > > (pet and cortical > > > >>> >>>>>> thickness relationship) using--pvr
> > > >>> >>>>>> To: Douglas N Greve > > > >>> >>>>>> > > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> >>>>>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> Hello Experts, > > > >>> >>>>>> > > > >>> >>>>>> I am performing an analysis > > > >>> looking at the > > > >>> >>>>>> relationship between amyloid > > uptake and > > > cortical > > > >>> >>>>>> thickness using --pvr flag in > > mri_glmfit. > > > I've 2 > > > >>> >>>>>> groups and 2 variables (age and > > education). I > > > >>> >>>>>> want to run a within group > > > >>> analysis while > > > >>> >>>>>> regressing out age and education > > (i.e. Within > > > >>> >>>>>> group 1, is there a negative > > > >>> relationship between > > > >>> >>>>>> amyloid uptake and cortical > > thickness > > > regressing > > > >>> >>>>>> out the effects of age and > > > >>> education). > > > >>> >>>>>> > > > >>> >>>>>> However, i'm not sure how my pvr > > contrasts > > > will > > > >>> >>>>>> look like. Below are my fsgd and > > > >>> an attempt at > > > >>> >>>>>> creating contrasts. Please, can > > you let me > > > know > > > >>> >>>>>> if my contrasts are correctbased
> > > >>> on my questions. > > > >>> >>>>>> > > > >>> >>>>>> Thank you. > > > >>> >>>>>> > > > >>> >>>>>> Best, > > > >>> >>>>>> Paul > > > >>> >>>>>> > > > >>> >>>>>> The fsgd file lists: > > > >>> >>>>>> > > > >>> > > ------------------------------------------------------------- > > > >>> >>>>>> GroupDescriptorFile 1 > > > >>> >>>>>> Title Relationship Amy-thick reg > > > >>> out age and education > > > >>> >>>>>> Class g1 > > > >>> >>>>>> Class g2 > > > >>> >>>>>> Variable Age Education > > > >>> >>>>>> Input XX1 g1 60 16 > > > >>> >>>>>> Input XX2 g1 58 14 > > > >>> >>>>>> Input YY1 g2 62 20 > > > >>> >>>>>> �� Input YY1 g2 62 20 > > > >>> >>>>>> > > > >>> > > ------------------------------------------------------------- > > > >>> >>>>>> matrix for group1: > > > >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 > > > >>> >>>>>> is there a relationship between > > > >>> amyloid-thickness in group1 regressing > > out age > > > >>> >>>>>> and education? > > > >>> >>>>>> matrix for group2: > > > >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 > > > >>> >>>>>> is there a relationship between > > > >>> amyloid-thickness in group2 regressing > > out age > > > >>> >>>>>> and education? > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > _______________________________________________ > > > >>> >>>>>> Freesurfer mailing list > > > >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>>>> > > > >>> >>>>> > > _______________________________________________ > > > >>> >>>>> Freesurfer mailing list > > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> >>>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>>>> > > > >>> >>>>> > > > >>> >>>>> > > _______________________________________________ > > > >>> >>>>> Freesurfer mailing list > > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu 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<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>>> > > > >>> >>>> > > _______________________________________________ > > > >>> >>>> Freesurfer mailing list > > > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu 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<mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> > > _______________________________________________ > > > >>> >>>> Freesurfer mailing list > > > >>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>> > > > >>> >>> > > > >>> >>> > > _______________________________________________ > > > >>> >>> Freesurfer mailing list > > > >>> >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >> > > > >>> >> > > _______________________________________________ > > > >>> >> Freesurfer mailing list > > > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu 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<mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >> > > > >>> >> > > > >>> >> > > _______________________________________________ > > > >>> >> Freesurfer mailing list > > > >>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> >> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> > > > > >>> > > > _______________________________________________ > > > >>> > Freesurfer mailing list > > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > >>> > > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> > > > > >>> > > > > >>> > > > _______________________________________________ > > > >>> > Freesurfer mailing list > > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> > > > >>> > > > >>> _______________________________________________ > > > >>> Freesurfer mailing list > > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> > > > >>> > > > >>> _______________________________________________ > > > >>> Freesurfer mailing list > > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >> > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >> > > > >> > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > 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2:36 p.m.
New subject: Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr
You just want to merge labels? I think those commands will work. But if you just want to merge, you can use the --replace option to mri_gtmpvc.
On 8/14/19 2:29 PM, miracle ozzoude wrote:
External Email - Use Caution
I will go the easy way. By 'compute mean" do you mean, using mri_annotation2label to get the label files, merge them using mri_mergelabels to them, smooth using mris_fwhm with --label , and run mri_glmfit with the --label. I tried something similar because the pet volumes are already in the surf. mri_vol2surf --mov $in_dir/${session}.gtmpvc.output/mgx.ctxgm.nii.gz --reg $in_dir/${session}.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 \ --o $in_dir/lh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage mri_vol2surf --mov $in_dir/${session}.gtmpvc.output/mgx.ctxgm.nii.gz --reg $in_dir/${session}.gtmpvc.output/aux/bbpet2anat.lta --hemi rh --projfrac 0.5 \ --o $in_dir/rh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage
##extract labels from fsaverage mri_annotation2label --subject fsaverage --hemi lh --outdir ${SUBJECTS_DIR}/fsaverage/label mri_annotation2label --subject fsaverage --hemi rh --outdir ${SUBJECTS_DIR}/fsaverage/label
# #merge the ROI to form global ROI. e.g frontal lobe # #right hemisphere mri_mergelabels -i ${SUBJECTS_DIR}/fsaverage/label/rh.precuneus.label -i ${SUBJECTS_DIR}/fsaverage/label/rh.posteriorcingulate.label \ -i ${SUBJECTS_DIR}/fsaverage/label/rh.isthmuscingulate.label -i ${SUBJECTS_DIR}/fsaverage/label/rh.insula.label \ -i ${SUBJECTS_DIR}/fsaverage/label/rh.medialorbitofrontal.label -i ${SUBJECTS_DIR}/fsaverage/label/rh.lateralorbitofrontal.label \ -o ${SUBJECTS_DIR}/fsaverage/label/rh.early.label # ##left hemisphere mri_mergelabels -i ${SUBJECTS_DIR}/fsaverage/label/lh.precuneus.label -i ${SUBJECTS_DIR}/fsaverage/label/lh.posteriorcingulate.label \ -i ${SUBJECTS_DIR}/fsaverage/label/lh.isthmuscingulate.label -i ${SUBJECTS_DIR}/fsaverage/label/lh.insula.label \ -i ${SUBJECTS_DIR}/fsaverage/label/lh.medialorbitofrontal.label -i ${SUBJECTS_DIR}/fsaverage/label/lh.lateralorbitofrontal.label \ -o ${SUBJECTS_DIR}/fsaverage/label/lh.early.label
# # # #concatenate all subjects mri_concat --f "$lhmgxctxgm" --o ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune mri_concat --f "$rhmgxctxgm" --o ${results_dir}/all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune
# # # # #smooth on the surface mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --prune --label ${SUBJECTS_DIR}/fsaverage/label/lh.early.label \ --i ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --o ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz mris_fwhm --smooth-only --s fsaverage --hemi rh --fwhm 5 --prune --label ${SUBJECTS_DIR}/fsaverage/label/rh.early.label \ --i ${results_dir}/all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --o ${results_dir}/all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz
# # # # # Run GLM analysis mri_glmfit --y ${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --fsgd $Pet_fsgd dods --C $martrix1 \ --surf fsaverage lh --label ${SUBJECTS_DIR}/fsaverage/label/lh.early.label --glmdir ${results_dir}/lh.pet.1.$Pet_fsgd.glmdir mri_glmfit --y ${results_dir}/all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz --fsgd $Pet_fsgd dods --C $martrix1 \ --surf fsaverage rh --label ${SUBJECTS_DIR}/fsaverage/label/rh.early.label --glmdir ${results_dir}/rh.pet.1.$Pet_fsgd.glmdir
On Wed, Aug 14, 2019 at 2:09 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
There are two ways, one easy, one hard. The easy way is to just use mri_vol2surf to sample on the surface, then compute the mean over any surface-based ROI that you want. The harder way is to create a new annotation, then run gtmseg again, then mri_gmptvc with the new gtmseg. On 8/14/19 1:15 PM, miracle ozzoude wrote: > > External Email - Use Caution > > the surface based pet analysis in the petsurfer link use the whole > brain. i want to do my surface base pet analysis on specific regions > of the aparc not the entire regions. Should i use mri_vol2label to > extract the covert the volume to labels, them mri_mergelabels to merge > them? Thanks. > > On Wed, Aug 14, 2019 at 1:08 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Then just do the standard PETsurfer processing > > On 8/14/19 12:59 PM, miracle ozzoude wrote: > > > > External Email - Use Caution > > > > I want to use the aparc ROI. something similar to doing ROI surface > > base cortical thickness analysis where i used > mri_annotation2label to > > extract the regions and mri_mergelabels to merge them and run > analysis > > on them. > > > > On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > Do you mean using different ROIs than in the aparc? If you > want to > > use > > the aparc, then that is done in the standard processing. > > > > On 8/14/19 11:16 AM, miracle ozzoude wrote: > > > > > > External Email - Use Caution > > > > > > Hey Doug, > > > > > > If i want to do ROI surface base PET analysis using the method > > on the > > > PETsurfer website. Please, how do i go about doing it? I > know there > > > series of commands i will need to run before project it to the > > surface > > > using mri_vol2surf. > > > thanks a lot > > > best, > > > Paul > > > > > > On Tue, Aug 13, 2019 at 11:00 AM miracle ozzoude > > <miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> wrote: > > > > > > Awesome. thanks a lot for your help. I appreciate it. > > > > > > Best, > > > Paul > > > > > > On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D. > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > wrote: > > > > > > You can use mri_surfcluster. That actually has an > --fdr > > flag, > > > so you > > > should not need to run mri_fdr. When you use > --fdr, you > > do not > > > use > > > --thmin. Use --sum to get the summary file > > > > > > On 8/13/19 10:50 AM, miracle ozzoude wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Thanks a lot doug. I want to use mri_fdr instead of > > > mri_glmfit-sim. > > > > How do i get a summary of clusters like > mri_glmfit-sim? I > > > searched > > > > through the forum and based on previous > responses, The > > > advice was to > > > > do mri_fdr and then use mri_surfcluster without > the fdr > > > option to > > > > obtain the summary of cluster. Is this correct? > > > > Paul > > > > > > > > On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas > N.,Ph.D. > > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> wrote: > > > > > > > > I don't know that there is much you can do. The > > PVR is very > > > > computationally intensive, and it does not > surprise me > > > that it is > > > > taking > > > > a long time. I don't think you need to do 10k > > > permutations. I would > > > > start with 1k. In the output, you will get a > > confidence > > > interval > > > > for the > > > > corrected p-value. This will shrink with the > number of > > > > permutations, but > > > > if you're happy with it, no need to do more > > > > > > > > On 8/13/19 10:17 AM, miracle ozzoude wrote: > > > > > > > > > > External Email - Use Caution > > > > > > > > > > Thanks Doug. My correction for multiple > comparison > > > using 10000 > > > > > permutation and abs has been running for > 3days. This > > > is strange > > > > > because i am using the --bg 10 and it > usually takes > > > 1hr to finish > > > > > without the --pvr. how do i solve this? > > > > > Below is my mri_glmfit and mri_glmfit-sim > commands > > > > > > > > > > mri_glmfit --y ${lhpetsurfimg} --fsgd > $bothgrpfsgd > > > dods --C $pvr1 > > > > > --pvr > ${wholebrain}/lh.$grp1fsgd.pvr.thickness.mgh \ > > > > > --pvr > > ${wholebrain}/lh.$grp2fsgd.pvr.thickness.mgh --surf > > > > fsaverage lh > > > > > --cortex \ > > > > > --glmdir ${wholebrain}/lh.pet.thickness.glmdir > > --eres-save > > > > > > > > > > mri_glmfit-sim --glmdir > > > ${wholebrain}/lh.pet.thickness.glmdir > > > > --perm > > > > > 10000 2 abs --perm-force --cwp 0.05 --2spaces > > --bg 10 > > > --overwrite > > > > > > > > > > > > > > > On Mon, Aug 12, 2019 at 11:31 AM Greve, > Douglas > > N.,Ph.D. > > > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> > > > > wrote: > > > > > > > > > > You will have to click on the vertex > you are > > > interested in. The > > > > > value will be -log10(pcorrected) where > > pcorrected > > > is the > > > > corrected > > > > > p-value > > > > > > > > > > On 8/12/2019 11:24 AM, miracle ozzoude > wrote: > > > > >> > > > > >> External Email - Use Caution > > > > >> > > > > >> these regions (please see below) came out > > > significant for the > > > > >> voxel-wise corrected map. I want to > know their > > > p-values. > > > > >> mri-glmfit-sim doesn't give summary > file for > > > voxel-wise > > > > corrected > > > > >> map only for cluster-wise map. > > > > >> image.png > > > > >> > > > > >> On Mon, Aug 12, 2019 at 11:19 AM > Greve, Douglas > > > N.,Ph.D. > > > > >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> > > > > wrote: > > > > >> > > > > >> I'm not sure what you are looking > for. The > > > voxel-wise > > > > >> analysis is voxel-wise, so there > is no > > > summary file for it > > > > >> > > > > >> On 8/12/2019 11:13 AM, miracle > ozzoude > > wrote: > > > > >>> > > > > >>> External Email - Use Caution > > > > >>> > > > > >>> Thanks Doug. Another question, > how do > > i find > > > the p-values > > > > >>> for voxel-wise map corrected for > multiple > > > comparisons at a > > > > >>> voxel (rather than cluster) level > > > > >>> (perm.th40.abs.sig.voxel.mgh). There is no > > summary > > > > file for it. > > > > >>> Best, > > > > >>> Paul > > > > >>> > > > > >>> On Wed, Aug 7, 2019 at 11:08 AM > Greve, > > > Douglas N.,Ph.D. > > > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> wrote: > > > > >>> > > > > >>> The 3 spaces is for left > hemi, right > > > hemi, and > > > > >>> subcortical, so, if you > > > > >>> are using all three then correct > > for all 3 > > > > >>> > > > > >>> On 8/7/19 9:26 AM, miracle > ozzoude > > wrote: > > > > >>> > > > > > >>> > External Email - > Use Caution > > > > >>> > > > > > >>> > Got it. Thanks a lot doug. > If i have > > > to correct for > > > > >>> multiple > > > > >>> > comparison in surface > based pet > > > analysis and > > > > >>> mutlimodal analysis (pet > > > > >>> > and thickness), should i use > > --3spaces? > > > > >>> > Thank you. > > > > >>> > > > > > >>> > best, > > > > >>> > Paul > > > > >>> > > > > > >>> > On Mon, Aug 5, 2019 at > 10:19 PM > > Greve, > > > Douglas > > > > N.,Ph.D. > > > > >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>>> wrote: > > > > >>> > > > > > >>> > I think there is still > something > > > not right. You > > > > >>> should just have > > > > >>> > one mri_glmfit command > for each > > > hemisphere in > > > > >>> which the input is > > > > >>> > ?h.thickness.15.mgh, the > > fsgdfile is > > > > project.fsgd, > > > > >>> you then > > > > >>> > specify the pvrs for both > groups > > > (--pvr > > > > >>> ?h.pvr_grp1_pet.nii.gz > > > > >>> > --pvr > ?h.pvr_grp2_pet.niigz) and > > > then use that > > > > >>> first contrast. The > > > > >>> > second is the same as > the first > > > but with a > > > > >>> reversed sign, but it > > > > >>> > is not necessary since > we always > > > use unsigned > > > > >>> tests and show both > > > > >>> > signs (but you can > still do it). > > > > >>> > > > > > >>> > On 8/5/2019 8:14 PM, > miracle > > > ozzoude wrote: > > > > >>> >> > > > > >>> >> External Email - Use > > Caution > > > > >>> >> > > > > >>> >> I think i got it now. Something > > > like this: > > > > >>> >> > > > > >>> >> ## group1 comes first in my > > fsgd > > > file. removing > > > > >>> the effects of > > > > >>> >> age and education > > > > >>> >> ##amyloid-thickness. first pet > > pvr = > > > 1 for > > > > group1 > > > > >>> and 0 for group 2. > > > > >>> >> mri_glmfit --y > > > lh.thickness.15.mgh --fsgd > > > > >>> project.fsgd dods --c > > > > >>> >> pvr1.mtx --pvr > > > lh.pvr_grp1_pet.nii.gz \ > > > > >>> >> --pvr > > > > >>> > > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > > >>> >> fsaverage lh --cortex --glmdir > > > > >>> lh.pet.thickness.glmdir > > > > >>> >> mri_glmfit --y > > > rh.thickness.15.mgh --fsgd > > > > >>> project.fsgd dods --c > > > > >>> >> pvr1.mtx --pvr > > > rh.pvr_grp1_pet.nii.gz \ > > > > >>> >> --pvr > > > > >>> > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > fsaverage > > > > >>> >> lh --cortex --glmdir > > > rh.pet.thickness.glmdir > > > > >>> >> > > > > >>> >> contrast = 0 0 0 0 0 0 1 -1 > > > > >>> >> > > > > >>> >> ##group 2 is second in my fsgd > > file. > > > > removing the > > > > >>> effects of age > > > > >>> >> and education > > > > >>> >> ##amyloid-thickness. first pet > > pvr = > > > 0 for > > > > group1 > > > > >>> and 1 for group2 > > > > >>> >> mri_glmfit --y > > > lh.thickness.15.mgh --fsgd > > > > >>> project.fsgd dods --c > > > > >>> >> pvr2.mtx --pvr > > > > >>> > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > > >>> >> --pvr lh.pvr_grp2_pet.nii.gz > > > -surf fsaverage lh > > > > >>> --cortex --glmdir > > > > >>> >> rh.pet.thickness.glmdir > > > > >>> >> mri_glmfit --y > > > rh.thickness.15.mgh --fsgd > > > > >>> project.fsgd dods --c > > > > >>> >> pvr2.mtx --pvr > > > > >>> > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > > >>> >> --pvr rh.pvr_grp2_pet.nii.gz > > > -surf fsaverage lh > > > > >>> --cortex --glmdir > > > > >>> >> rh.pet.thickness.glmdir > > > > >>> >> > > > > >>> >> contrast = 0 0 0 0 0 0 -1 1 > > > > >>> >> > > > > >>> >> On Mon, Aug 5, 2019 at 6:47 PM > > > Greve, Douglas > > > > >>> N.,Ph.D. > > > > >>> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>>> wrote: > > > > >>> >> > > > > >>> >> It still looks like you are > > > using a group > > > > >>> specific input > > > > >>> >> (--y). The input should be a > > > simple > > > > file with > > > > >>> both groups > > > > >>> >> (same input as you would use > > > without pvr) > > > > >>> >> > > > > >>> >> On 8/5/2019 4:39 PM, > > > miracooloz wrote: > > > > >>> >>> > > > > >>> >>> External Email - Use > > Caution > > > > >>> >>> > > > > >>> >>> Thanks Doug. How about the > > mri_glmfit > > > > >>> commands? Since the > > > > >>> >>> contrasts are correct, I > > think the > > > > commands > > > > >>> should be right. > > > > >>> >>> > > > > >>> >>> Best, > > > > >>> >>> Paul. > > > > >>> >>> > > > > >>> >>> > > > > >>> >>> > > > > >>> >>> Sent from my Samsung Galaxy > > smartphone. > > > > >>> >>> > > > > >>> >>> -------- Original message > > -------- > > > > >>> >>> From: "Greve, Douglas N.,Ph.D." > > > > >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> > > > > >>> >>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>> > > > > >>> >>> Date: 2019-08-05 15:52 > > (GMT-05:00) > > > > >>> >>> To: > > > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > > >>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>> > > > > >>> >>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > > >>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>>> > > > > >>> >>> Subject: Re: [Freesurfer] Fwd: > > > multimodal > > > > >>> analysis (pet and > > > > >>> >>> cortical thickness > > relationship) using > > > > --pvr > > > > >>> >>> > > > > >>> >>> Yes, that contrast is correct. > > > > >>> >>> > > > > >>> >>> On 8/5/2019 3:11 PM, miracle > > > ozzoude > > > > wrote: > > > > >>> >>>> > > > > >>> >>>> External Email - Use Caution > > > > >>> >>>> > > > > >>> >>>> Hello Doug, > > > > >>> >>>> > > > > >>> >>>> Thanks very much for your help. Your > > > > >>> assumption was right > > > > >>> >>>> in that i want to run a group > > > comparison > > > > >>> (i.e. test for a > > > > >>> >>>> difference in amyloid-thickness > slopes > > > > >>> between the two > > > > >>> >>>> groups). However, I am having a > > > hard time > > > > >>> creating the > > > > >>> >>>> correct mri_glmfit and contrasts > > > in this > > > > >>> case. Based on > > > > >>> >>>> your advice and searching through the > > > > forum > > > > >>> >>>> > > > > >>> > > > > > > > > > > (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html), i > > > > >>> >>>> need 2 PVRs for each hemisphere > in the > > > > >>> mri_glmfit command. > > > > >>> >>>> I gave it another shot below. Please > > > > let me > > > > >>> know if i am > > > > >>> >>>> correct. > > > > >>> >>>> > > > > >>> >>>> Thank you. > > > > >>> >>>> Paul. > > > > >>> >>>> > > > > >>> >>>> ## group1 comes first in my fsgd > file. > > > > >>> removing the effects > > > > >>> >>>> of age and education > > > > >>> >>>> ##amyloid-thickness. first pet pvr > > > = 1 for > > > > >>> group1 and 0 for > > > > >>> >>>> group 2. > > > > >>> >>>> mri_glmfit --y > > > > lh_pvr_grp1_thickness.mgh --fsgd > > > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > > > >>> lh.pvr_grp1_pet.nii.gz \ > > > > >>> >>>> --pvr > > > > >>> > > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > > >>> >>>> fsaverage lh --cortex --glmdir > > > > >>> lh.pet.thickness.glmdir > > > > >>> >>>> mri_glmfit --y > > > > rh_pvr_grp1_thickness.mgh --fsgd > > > > >>> >>>> project.fsgd dods --c pvr1.mtx --pvr > > > > >>> rh.pvr_grp1_pet.nii.gz \ > > > > >>> >>>> --pvr > > > > >>> > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > > > > >>> >>>> fsaverage lh --cortex --glmdir > > > > >>> rh.pet.thickness.glmdir > > > > >>> >>>> > > > > >>> >>>> contrast = 0 0 0 0 0 0 1 -1 > > > > >>> >>>> > > > > >>> >>>> ##group 2 is second in my fsgd file. > > > > >>> removing the effects > > > > >>> >>>> of age and education > > > > >>> >>>> ##amyloid-thickness. first pet pvr > > > = 0 for > > > > >>> group1 and 1 for > > > > >>> >>>> group2 > > > > >>> >>>> mri_glmfit --y > > > > >>> lh_pvr_grp2_thickness.mgh --fsgd > > > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > > > >>> >>>> > > > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > > >>> >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf > > > > >>> fsaverage lh --cortex > > > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > > > >>> >>>> mri_glmfit --y > > > > rh_pvr_grp2_thickness.mgh --fsgd > > > > >>> >>>> project.fsgd dods --c pvr2.mtx --pvr > > > > >>> >>>> > > > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > > > > >>> >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf > > > > >>> fsaverage lh --cortex > > > > >>> >>>> --glmdir rh.pet.thickness.glmdir > > > > >>> >>>> > > > > >>> >>>> contrast = 0 0 0 0 0 0 -1 1 > > > > >>> >>>> > > > > >>> >>>> > > > > >>> >>>> On Mon, Aug 5, 2019 at 12:26 PM > Greve, > > > > >>> Douglas N.,Ph.D. > > > > >>> >>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>>> wrote: > > > > >>> >>>> > > > > >>> >>>> That mostly looks good. > > > > >>> >>>> > > > > >>> >>>> I would suggest is to change your > > > > >>> smoothing command to > > > > >>> >>>> something like > > > > >>> >>>> mris_fwhm --smooth-only --s fsaverage > > > > >>> --hemi lh --fwhm > > > > >>> >>>> 5 --cortex --prune --i > > > > >>> >>>> > > > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > > > >>> >>>> > allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > > >>> >>>> The only difference will be > > > that any > > > > >>> vertices that are > > > > >>> >>>> 0 in the input will be excluded > > > > >>> (pruned) from the > > > > >>> >>>> smoothing mask. > > > > >>> >>>> > > > > >>> >>>> The mri_glmfit command is not > > > right. > > > > >>> That command looks > > > > >>> >>>> like it is for analyzing each > > > group > > > > >>> separately and > > > > >>> >>>> independently. If that is what you > > > want > > > > >>> to do, then you > > > > >>> >>>> don't need to go through all the > > > > extra > > > > >>> stuff of > > > > >>> >>>> creating zero files, etc. I had > > > > assumed > > > > >>> that you wanted > > > > >>> >>>> to do some kind of comparison > > > between > > > > >>> groups. If so, > > > > >>> >>>> then you would use a single > > > file with > > > > >>> all your data in > > > > >>> >>>> it (probably what you were using > > > > >>> before), and your fsgd > > > > >>> >>>> file would have both groups. > > > > >>> >>>> > > > > >>> >>>> 1) will my fsgd file contain both > > > > groups? > > > > >>> >>>> yes, see above > > > > >>> >>>> 2) If the answer from question is > > > > yes, > > > > >>> i should have 2 > > > > >>> >>>> contrasts (pvr1.mtx for group1 and > > > > >>> pvr2.mtx for > > > > >>> >>>> group2). yes/no? > > > > >>> >>>> Again, if all you want to do is > > > > to test > > > > >>> the pvr for > > > > >>> >>>> each group separately, then > > > you don't > > > > >>> need to go > > > > >>> >>>> through the processes of creating > > > > zero > > > > >>> files, etc. In > > > > >>> >>>> any event, if you want to test > > > a pvr, > > > > >>> then you need a > > > > >>> >>>> contrast for it. > > > > >>> >>>> 3) below is a sample of my > > > fsgd file. > > > > >>> are the > > > > >>> >>>> constrasts correct? > > > > >>> >>>> hard to say without resolving the > > > > >>> questions above. You > > > > >>> >>>> will need to have a value in the > > > > >>> contrast for each pvr. > > > > >>> >>>> > > > > >>> >>>> > > > > >>> >>>> > > > > >>> >>>> On 8/2/2019 3:56 PM, miracle > > > > ozzoude wrote: > > > > >>> >>>>> > > > > >>> >>>>> External Email - Use Caution > > > > >>> >>>>> > > > > >>> >>>>> Hello Doug, > > > > >>> >>>>> > > > > >>> >>>>> Thanks for answering. Based on your > > > > >>> explanation, i > > > > >>> >>>>> wrote out a series of command needed > > > > >>> to execute this. > > > > >>> >>>>> Please let me know if i made any > > > > >>> mistakes/correct. > > > > >>> >>>>> ##step1 concatenating the 10 amyloid > > > > >>> pet volumes files > > > > >>> >>>>> projected to surface using > > > > >>> mri_vol2surf for group1 > > > > >>> >>>>> mri_concat --f grp1.lhmgxctx --o > > > > >>> >>>>> > > > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > > > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > > > >>> >>>>> > > > allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > > > > >>> >>>>> > > > > >>> >>>>> ##step2 concatenating the 20 amyloid > > > > >>> pet volumes files > > > > >>> >>>>> projected to surface using > > > > >>> mri_vol2surf for group2 > > > > >>> >>>>> mri_concat --f grp2.lhmgxctx --o > > > > >>> >>>>> > > > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > > > > >>> >>>>> mri_concat --f grp2.rhmgxctx --o > > > > >>> >>>>> > > > allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > > > > >>> >>>>> > > > > >>> >>>>> ##step3 smooth on the surface for > > > each > > > > >>> hemisphere for > > > > >>> >>>>> group1 > > > > >>> >>>>> mri_surf2surf --hemi lh --s > fsaverage > > > > >>> --sval > > > > >>> >>>>> > > > allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > > > >>> >>>>> --cortex --tval > > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > > >>> >>>>> mri_surf2surf --hemi rh --s > fsaverage > > > > >>> --sval > > > > >>> >>>>> > > > allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > > > > --fwhm 5 > > > > >>> >>>>> --cortex --tval > > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > > > >>> >>>>> > > > > >>> >>>>> ##step4 smooth on the surface for > > > each > > > > >>> hemisphere for > > > > >>> >>>>> group2 > > > > >>> >>>>> mri_surf2surf --hemi lh --s > fsaverage > > > > >>> --sval > > > > >>> >>>>> > > > allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > > > > >>> >>>>> --cortex --tval > > > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > > > > >>> >>>>> mri_surf2surf --hemi rh --s > fsaverage > > > > >>> --sval > > > > >>> >>>>> > > > allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz > > > > --fwhm 5 > > > > >>> >>>>> --cortex --tval > > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > > > > >>> >>>>> > > > > >>> >>>>> ##step5 create files of zeros for > > > > >>> group1 for each > > > > >>> >>>>> hemisphere > > > > >>> >>>>> fscalc > > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > mul 0 -o > > > > >>> >>>>> > > > allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > > > >>> >>>>> fscalc > > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > mul 0 -o > > > > >>> >>>>> > > > allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > > > >>> >>>>> > > > > >>> >>>>> ##step6 create files of zeros for > > > > >>> group2 for each > > > > >>> >>>>> hemisphere > > > > >>> >>>>> fscalc > > > > >>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > mul 0 -o > > > > >>> >>>>> > > > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > > > > >>> >>>>> fscalc > > > > >>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > mul 0 -o > > > > >>> >>>>> > > > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > > > > >>> >>>>> > > > > >>> >>>>> ##step7 create pvr files for group1 > > > > >>> for each hemisphere > > > > >>> >>>>> mri_concat > > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > > > > >>> >>>>> > > > allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > > > > >>> >>>>> lh.pvr_grp1_pet.nii.gz > > > > >>> >>>>> mri_concat > > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > > > > >>> >>>>> > > > allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > > > > >>> >>>>> rh.pvr_grp1_pet.nii.gz > > > > >>> >>>>> > > > > >>> >>>>> ##step8 create pvr files for group2 > > > > >>> for each hemisphere > > > > >>> >>>>> mri_concat > > > > >>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > > > > >>> >>>>> > > > allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > > > > >>> >>>>> lh.pvr_grp2_pet.nii.gz > > > > >>> >>>>> mri_concat > > > > >>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > > > > >>> >>>>> > > > allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > > > > >>> >>>>> rh.pvr_grp2_pet.nii.gz > > > > >>> >>>>> > > > > >>> >>>>> ###-----repeat steps 1-8 for > > > cortical > > > > >>> thickness------- > > > > >>> >>>>> > > > > >>> >>>>> ###run glm-fit for group1 > > > > >>> >>>>> mri_glmfit --y > lh.pvr_grp1_pet.nii.gz > > > > >>> --fsgd > > > > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > > > > >>> >>>>> lh_pvr_grp1_thickness.mgh --surf > > > fsaverage lh > > > > >>> --cortex > > > > >>> >>>>> --glmdir > lh.grp1.pet.thickness.glmdir > > > > >>> >>>>> mri_glmfit --y > rh.pvr_grp1_pet.nii.gz > > > > >>> --fsgd > > > > >>> >>>>> project.fsgd dods --c pvr1.mtx --pvr > > > > >>> >>>>> rh_pvr_grp1_thickness.mgh --surf > > > fsaverage lh > > > > >>> --cortex > > > > >>> >>>>> --glmdir > rh.grp1.pet.thickness.glmdir > > > > >>> >>>>> > > > > >>> >>>>> ###run glm-fit for group2 > > > > >>> >>>>> mri_glmfit --y > lh.pvr_grp2_pet.nii.gz > > > > >>> --fsgd > > > > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > > > > >>> >>>>> lh_pvr_grp2_thickness.mgh --surf > > > fsaverage lh > > > > >>> --cortex > > > > >>> >>>>> --glmdir > lh.grp2.pet.thickness.glmdir > > > > >>> >>>>> mri_glmfit --y > rh.pvr_grp2_pet.nii.gz > > > > >>> --fsgd > > > > >>> >>>>> project.fsgd dods --c pvr2.mtx --pvr > > > > >>> >>>>> rh_pvr_grp2_thickness.mgh --surf > > > fsaverage lh > > > > >>> --cortex > > > > >>> >>>>> --glmdir > rh.grp2.pet.thickness.glmdir > > > > >>> >>>>> > > > > >>> >>>>> My questions. > > > > >>> >>>>> 1) will my fsgd file contain > > > > both groups? > > > > >>> >>>>> 2) If the answer from > > > question > > > > is yes, > > > > >>> i should have 2 > > > > >>> >>>>> contrasts (pvr1.mtx for group1 and > > > > >>> pvr2.mtx for > > > > >>> >>>>> group2). yes/no? > > > > >>> >>>>> 3) below is a sample of > > > my fsgd > > > > file. > > > > >>> are the > > > > >>> >>>>> constrasts correct? > > > > >>> >>>>> > > > > >>> >>>>> Thank you very much. > > > > >>> >>>>> Paul. > > > > >>> >>>>> The fsgd file lists: > > > > >>> >>>>> > > > > >>> > > > > ------------------------------------------------------------- > > > > >>> >>>>> GroupDescriptorFile 1 > > > > >>> >>>>> Title Relationship Amy-thick reg out > > > > >>> age and education > > > > >>> >>>>> Class g1 > > > > >>> >>>>> Class g2 > > > > >>> >>>>> Variable Age Education > > > > >>> >>>>> Input XX1 g1 60 16 > > > > >>> >>>>> Input YY1 g2 62 20 > > > > >>> >>>>> > > > > >>> > > > > ------------------------------------------------------------- > > > > >>> >>>>> matrix for group1: > > > > >>> >>>>> pvr1.mtx= 1 0 0 0 0 0 0 > > > > >>> >>>>> is there a relationship > > > between > > > > >>> amyloid-thickness in group1 regressing > > > out age > > > > >>> >>>>> and education? > > > > >>> >>>>> matrix for group2: > > > > >>> >>>>> pvr2.mtx= 0 1 0 0 0 0 0 > > > > >>> >>>>> is there a relationship > > > between > > > > >>> amyloid-thickness in group2 regressing > > > out age > > > > >>> >>>>> and education? > > > > >>> >>>>> > > > > >>> >>>>> On Thu, Aug 1, 2019 at > > > 9:44 PM > > > > Greve, > > > > >>> Douglas N.,Ph.D. > > > > >>> >>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>> > > > > >>> >>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > > > >>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>>>>> wrote: > > > > >>> >>>>> > > > > >>> >>>>> Each PVR adds a single column to > > > > >>> the design > > > > >>> >>>>> matrix. In a two group design, > > > > >>> this can make it > > > > >>> >>>>> tricky to set up. Let's say you > > > > >>> have 10 of group1 > > > > >>> >>>>> and 20 of group2. You will need to > > > > >>> create two PVR > > > > >>> >>>>> files, each with 30=10+20 frames. > > > > >>> In the first > > > > >>> >>>>> one, the first 10 frames will be > > > > >>> cortical > > > > >>> >>>>> thickness (or amyloid sampled on > > > > >>> the surface) of > > > > >>> >>>>> group1; the next 20 frames will be > > > > >>> all zeros. For > > > > >>> >>>>> the 2nd PVR, the first 10 frames > > > > >>> will be 0s and > > > > >>> >>>>> the next 20 frames will be the > > > > >>> cortical thickness > > > > >>> >>>>> (or amyloid) for group2. I would > > > > >>> start by running > > > > >>> >>>>> mris_preproc for the two groups > > > separate (so 2 > > > > >>> >>>>> files, one with 10 frames the > > > > >>> other 20 frames). > > > > >>> >>>>> Then create the file of zeros using > > > > >>> >>>>> fscalc group2.mgz mul 0 -o > > > > >>> group2.zeros.mgz > > > > >>> >>>>> Then > > > > >>> >>>>> mri_concat group1.mgz > > > group2.zeros.mgz --o > > > > pvr1.mgz > > > > >>> >>>>> Then create the contrast based on > > > > >>> the FSGD, but > > > > >>> >>>>> then add two more numbers, one for > > > > >>> PVR1 (which > > > > >>> >>>>> tests for the within group > > > > >>> correlation), and one > > > > >>> >>>>> for PVR2 > > > > >>> >>>>> > > > > >>> >>>>> > > > > >>> >>>>> On 8/1/2019 3:14 PM, miracle > > > > >>> ozzoude wrote: > > > > >>> >>>>>> > > > > >>> >>>>>> External Email - Use > Caution > > > > >>> >>>>>> > > > > >>> >>>>>> Please, can anyone help me with > > > this. > > > > >>> >>>>>> Thank you > > > > >>> >>>>>> > > > > >>> >>>>>> Paul > > > > >>> >>>>>> > > > > >>> >>>>>> ---------- Forwarded message > > > --------- > > > > >>> >>>>>> From: *miracle ozzoude* > > > > >>> <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>>> > > > > >>> >>>>>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> > > > > >>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>>>>> > > > > >>> >>>>>> Date: Wed, Jul 31, 2019 at > 2:11 PM > > > > >>> >>>>>> Subject: multimodal analysis > > > (pet and cortical > > > > >>> >>>>>> thickness relationship) using --pvr > > > > >>> >>>>>> To: Douglas N Greve > > > > >>> >>>>>> > > > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > > >>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>> > > > > >>> >>>>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > > >>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>>>> > > > > >>> >>>>>> > > > > >>> >>>>>> > > > > >>> >>>>>> Hello Experts, > > > > >>> >>>>>> > > > > >>> >>>>>> I am performing an analysis > > > > >>> looking at the > > > > >>> >>>>>> relationship between amyloid > > > uptake and > > > > cortical > > > > >>> >>>>>> thickness using --pvr flag in > > > mri_glmfit. > > > > I've 2 > > > > >>> >>>>>> groups and 2 variables (age and > > > education). I > > > > >>> >>>>>> want to run a within group > > > > >>> analysis while > > > > >>> >>>>>> regressing out age and education > > > (i.e. Within > > > > >>> >>>>>> group 1, is there a negative > > > > >>> relationship between > > > > >>> >>>>>> amyloid uptake and cortical > > > thickness > > > > regressing > > > > >>> >>>>>> out the effects of age and > > > > >>> education). > > > > >>> >>>>>> > > > > >>> >>>>>> However, i'm not sure how my pvr > > > contrasts > > > > will > > > > >>> >>>>>> look like. Below are my fsgd and > > > > >>> an attempt at > > > > >>> >>>>>> creating contrasts. Please, can > > > you let me > > > > know > > > > >>> >>>>>> if my contrasts are correct based > > > > >>> on my questions. > > > > >>> >>>>>> > > > > >>> >>>>>> Thank you. > > > > >>> >>>>>> > > > > >>> >>>>>> Best, > > > > >>> >>>>>> Paul > > > > >>> >>>>>> > > > > >>> >>>>>> The fsgd file lists: > > > > >>> >>>>>> > > > > >>> > > > > ------------------------------------------------------------- > > > > >>> >>>>>> GroupDescriptorFile 1 > > > > >>> >>>>>> Title Relationship Amy-thick reg > > > > >>> out age and education > > > > >>> >>>>>> Class g1 > > > > >>> >>>>>> Class g2 > > > > >>> >>>>>> Variable Age Education > > > > >>> >>>>>> Input XX1 g1 60 16 > > > > >>> >>>>>> Input XX2 g1 58 14 > > > > >>> >>>>>> Input YY1 g2 62 20 > > > > >>> >>>>>> �� Input YY1 g2 62 20 > > > > >>> >>>>>> > > > > >>> > > > > ------------------------------------------------------------- > > > > >>> >>>>>> matrix for group1: > > > > >>> >>>>>> pvrgroup1= 1 0 0 0 0 0 0 > > > > >>> >>>>>> is there a relationship between > > > > >>> amyloid-thickness in group1 regressing > > > out age > > > > >>> >>>>>> and education? > > > > >>> >>>>>> matrix for group2: > > > > >>> >>>>>> pvrgroup2= 0 1 0 0 0 0 0 > > > > >>> >>>>>> is there a relationship between > > > > >>> amyloid-thickness in group2 regressing > > > out age > > > > >>> >>>>>> and education? > > > > >>> >>>>>> > > > > >>> >>>>>> > > > > >>> >>>>>> > > > > >>> >>>>>> > > > > >>> >>>>>> > > > > _______________________________________________ > > > > >>> >>>>>> Freesurfer mailing list > > > > >>> >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > >>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > > >>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > >>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>>> > > > > >>> >>>>>> > > > > >>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >>> >>>>> > > > > >>> >>>>> > > > _______________________________________________ > > > > >>> >>>>> Freesurfer mailing list > > > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > 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<mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > > >>> >>>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu 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_______________________________________________ > > > > >>> >>>>> Freesurfer mailing list > > > > >>> >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu 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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >> > > > > >> > > > > >> > _______________________________________________ > > > > >> Freesurfer mailing list > > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu 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> > > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu 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> > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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participants (4)
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Greve, Douglas N.,Ph.D. -
Greve, Douglas N.,Ph.D.
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miracle ozzoude -
miracooloz