External Email - Use Caution
Awesome. thanks a lot for your help. I appreciate it.Best,PaulOn 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 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?
> >>> >>>>>>
> >>> >>>>>>
> >>> >>>>>>
> >>> >>>>>>
> >>> >>>>>>
> _______________________________________________
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> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
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