Re: [Freesurfer] mri_glmfit --mask ERROR: dimension mismatch 1 between y and mask

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
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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