On 05/12/2016 05:46 AM, Mahtab Farahbakhsh wrote:
> Dear freeSurfer,
>
> I have problems with defining new labels for my brain scan or even of
> fsaverage. I need to define a new label (ROI) to be able to find the
> grey matter thickness for that specific region.
>
> My first problem is that when I define a new label on fsaverage, it
> does not save it for me and it gives me the following error:
>
> mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz,
> -1): could not open file
> /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could
> not open label file
> /Applications/freesurfer/subjects/fsaverage/label/ROI_test.label
>
> I intend to define a new label (ROI) on fsaverage and then use the
> mri_labe2label command to copy it on my desired structural MRI image.
> But it does not work for me.
How are you doing this? What tool are you using? What steps with the
tool are you executing?
>
> My second problem is that when I define a new label on my subject's
> MRI image and I run the mri_anatomical_stats with the label of my
> subject, it does not give me any output and this is what I get:
>
> bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh
> limiting computations to label anon/label/lh.test.label.
> reading volume
> /Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz...
> reading input surface
> /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
> reading input pial surface
> /Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial...
> reading input white surface
> /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
>
> and the error is that it could not find the file lh.test.label,
> however I can see it in the label folder.
Use the -b or -f flags to specify an output
>
> Please guide me with this issue.
>
> Best Regards,
> Mahtab.
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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