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. > <dgr...@mgh.harvard.edu <mailto:dgr...@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. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@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. > >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@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. > >>> <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@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. > >>> > <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@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. > >>> >> <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@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." > >>> <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>>> > >>> >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@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. > >>> >>>> <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@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. > >>> >>>>> <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>> > >>> >>>>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@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* > >>> <miracoo...@gmail.com > <mailto:miracoo...@gmail.com> <mailto:miracoo...@gmail.com > <mailto:miracoo...@gmail.com>> > >>> >>>>>> <mailto:miracoo...@gmail.com > <mailto:miracoo...@gmail.com> > >>> <mailto:miracoo...@gmail.com > <mailto:miracoo...@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 > <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 > >>> >> > >>> >> > >>> >> 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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>> > >> 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>> > > 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