On Fri, Jul 22, 2016 at 2:09 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

then you need to add --surface fsaverage lh to the mri_glmfit command
line, otherwise it thinks it is a volume-based analysis

On 07/22/2016 01:58 PM, Mihaela Stefan wrote:
> It's surface-based analysis.
>
> On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> Are you doing volume or surface-based analysis? If volume, then you'll
> need a volume mask and the --label is not appropriate.
>
> On 07/22/2016 01:36 PM, Mihaela Stefan wrote:
> > I tried that, too and it seemed to work. I extracted the ROIs from
> > ?h.aparc.annot and merged them into a single label with
> > mri_mergelabels then I ran mri_glmfit. Now I am not sure I used the
> > correct command to mask the search:
> >
> > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C
> > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir
> > lh.group_diff_g2v0.glmdir
> >
> > So I used my own label instead of ?h.aparc.annot. Does the above
> > command look right?
> >
> > Thanks again!
> > Mihaela
> >
> > On Fri, Jul 22, 2016 at 12:34 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > What was your visualization command? You should probably run
> > mri_vol2surf with --projfract 0.5 and --interp nearest to get a
> > surface
> > map. But it begs the question as to why you would do
> binarize the
> > aparc+aseg to get surface ROIs (you should just use the
> > ?h.aparc.annot).
> > doug
> >
> > On 07/22/2016 10:38 AM, Mihaela Stefan wrote:
> > > Hi Doug,
> > >
> > > I used this command:
> > > mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026
> > 1018 1020
> > > 1019 --i aparc+aseg.mgz --o lh22mask.mgz
> > >
> > > When I checked it first time, I opened it as a volume and
> it looked
> > > okay to me.
> > > Now I was able to view it in tksurfer but it looks weird. See
> > attachment.
> > >
> > >
> > > Alternatively, I was able to create a label with
> mri_mergelabels:
> > > mri_mergelabels -i rh.insula.label -i
> rh.superiorfrontal.label -i
> > > rh.caudalmiddlefrontal.label -i
> rh.rostralmiddlefrontal.label -i
> > > rh.supramarginal.label -i rh.inferiorparietal.label -i
> > > rh.caudalanteriorcingulate.label -i
> > rh.rostralanteriorcingulate.label
> > > -i rh.parsopercularis.label -i rh.parstriangularis.label -i
> > > rh.parsorbitalis.label -o rh.22mask.label
> > >
> > > The mri_glmfit command seemed to have run successfully.
> However, the
> > > results from the ROI analysis are almost identical with
> the whole
> > > brain analysis. I find that surprising. Does it make sense
> > statistically?
> > >
> > > Here is the command I used for the whole brain analysis:
> > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd
> dods --C
> > > group.diff.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.group_diff_g2v0WB.glmdir
> > >
> > > And the command with the label for the ROI analysis:
> > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd
> dods --C
> > > group.diff.mtx --surf fsaverage lh --label lh.22mask.label
> --glmdir
> > > lh.group_diff_g2v0.glmdir
> > >
> > > Thanks!
> > > Mihaela
> > >
> > >
> > > On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve
> > > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> > >
> > > How did you create the mask? It should be a surface
> overlay in
> > > fsaverage
> > > space, ie, you should be able to view it with
> > >
> > > tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1
> > >
> > > On 07/21/2016 01:51 PM, Mihaela Stefan wrote:
> > > > Hello freesurfers,
> > > >
> > > > I would like to use mri_glmfit with --mask but I get
> this
> > error:
> > > > dimension mismatch 1 between y and mask.
> > > > I created a binary mask from 22 aparc labels (using
> > > mri_binarize) and
> > > > I would like to run a surface-based analysis only on
> those
> > regions.
> > > > The command I use is:
> > > >
> > > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd
> > dods --C
> > > > lh.group.diff.mtx --surf fsaverage lh --mask
> lh22mask.mgz
> > --glmdir
> > > > lh.group_diff_g2v0.glmdir
> > > >
> > > > The input file was generated with this command:
> > > > mris_preproc --fsgd g2v0.fsgd --cache-in
> > thickness.fwhm15.fsaverage
> > > > --target fsaverage --hemi lh --out
> lh.g2v0.thickness.15.mgh
> > > >
> > > > From the error, it seems that I am not using the right
> > input file.
> > > > What kind of input file should be used with a mask?
> > > >
> > > > I also thought to use --label but I am not sure how to
> > combine my 22
> > > > labels in one single label. mris_label2annot can
> combine them
> > > but the
> > > > output is an annotation file not a label.
> > > >
> > > > As a note, we will want to do FDR correction, not MC.
> > > >
> > > > Thanks!
> > > > Mihaela
> > > >
> > > >
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> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
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> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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MGH-NMR Center
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