14 Aug
2019
14 Aug
'19
11:16 a.m.
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 >>> >>>>> >>> >>>>>
>>> >>>>> 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>> >>> >>>> <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>> >>> >> <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> <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 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