On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve <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>> 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>>> 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
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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