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 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> 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>> 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?
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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