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. < [email protected]> 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. < > [email protected]> 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 <[email protected]> >> Date: Wed, Jul 31, 2019 at 2:11 PM >> Subject: multimodal analysis (pet and cortical thickness relationship) >> using --pvr >> To: Douglas N Greve <[email protected]> >> >> >> 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 >> [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
