On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

Do you mean using different ROIs than in the aparc? If you want to use
the aparc, then that is done in the standard processing.

On 8/14/19 11:16 AM, miracle ozzoude wrote:
>
>         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
> <mailto: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 <mailto: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>
> <mailto: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>>
> > <mailto: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>>
> > <mailto: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>>
> <mailto: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>>>
> > >>> <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
> <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>>>
> > >>> <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
> <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>>>>
> > >>> >>> <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
> <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>>>
> > >>> >>>
>   <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
> <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>>>
> > >>> <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
> <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>>>
> > >>> >>>>> <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
> <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>>>
> > >>> >>>>>> <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
> <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>>>
> > >>> >>>>>>
>   <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
> <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>>>
> > >>> <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
> <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>>>
> > >>> >>>>>
>   <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
> <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>>>
> > >>> <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
> <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>>>
> > >>> >>>>
>   <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
> <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>>>
> > >>> <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
> <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>>>
> > >>> <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
> <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>>>
> > >>> >>
>   <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
> <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>>>
> > >>> <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
> <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>>>
> > >>> <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
> <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>
> > 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