External Email - Use Caution
Then just do the standard PETsurfer processing
On 8/14/19 12:59 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
>
> I want to use the aparc ROI. something similar to doing ROI surface
> base cortical thickness analysis where i used mri_annotation2label to
> extract the regions and mri_mergelabels to merge them and run analysis
> on them.
>
> On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto: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>
> > <mailto: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>
> <mailto: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>>
> > <mailto: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>>>
> > > <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:
> > > >
> > > > 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>>>
> > > <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'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>>>
> > <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:
> > > >>>
> > > >>> 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>>>>
> > > >>> <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
> <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>>>>
> > > >>> <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
> <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>>>>>
> > > >>> >>>
> <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
> <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>>>>
> > > >>> >>>
> > <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
> <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>>>>
> > > >>> <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
> <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>>>>
> > > >>> >>>>> <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
> <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>>>>
> > > >>> >>>>>> <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
> <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>>>>
> > > >>> >>>>>>
> > <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
> <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>>>>
> > > >>>
> <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
> <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>>>>
> > > >>> >>>>>
> > <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
> <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>>>>
> > > >>>
> <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
> <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>>>>
> > > >>> >>>>
> > <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
> <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>>>>
> > > >>>
> <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
> <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>>>>
> > > >>>
> <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
> <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>>>>
> > > >>> >>
> > <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
> <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>>>>
> > > >>>
> <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
> <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>>>>
> > > >>>
> <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
> <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>>
> > >
> 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