Dear freeSurfer,

Thank you. I can use mris_anatomical_stats for the labels that are already defined, but when I want to define a new label, it does not work.

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.

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.

Please guide me with this issue.

Best Regards, Mahtab.

On 6 May 2016 at 16:45, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

If you have a label, then you can use mris_anatomical_stats with the -l option doug

On 05/06/2016 10:01 AM, Mahtab Farahbakhsh wrote:

...

Dear FreeSurfer,

I am trying to find the cortical thickness of my ROI which is the perisylvian region of the left hemisphere. What I did was to define a label based on the anatomical area of this region and tried to define a ROI based on this label and the command -mri_label2volume. Howevere, I am using freeview and the tutorial that I found about this issue was based on tkmedit. Would you please guide me how I should get this done?

Best Regards, Mahtab Farahbakhsh.

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