Dear Douglas,

To define my new label, I choose the ROI section and choose "New ROI". Then I save it, but it doesn't work properly. In addition, I cant save it on fsaverage.

Best Regards, Mahtab.

On 12 May 2016 at 22:08, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

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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