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Hi Doug,

I used the command below to convert a volume to a label file. The volume is a binary mask highlighting a subcortical ROI that I am projecting to the closest vertex. I can visualize the label on the fsaverage lh.white surface. mri_vol2label --i /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/rh.custom.nii --id 1 --l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label

Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

On Apr 24, 2019, at 9:48 AM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote:

How did you create the label? Is it a surface-based label? Ie, does it have valid vertex indices as the first item in each label point in the label file?

On 4/24/2019 2:44 AM, Nillo, Ryan Michael R wrote:

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Hello Freesurfer developers,

I am using the code below to generate the stats table for the ROI. mris_anatomical_stats -l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label -b subject rh white

However, when I run this command, I get this output:

limiting computations to label /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label. reading volume /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/wm.mgz... reading input surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... reading input pial surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.pial... reading input white surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white...

table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name

I am getting no values for any of the metrics listed above. Is this a bug?

Thanks in advance,

Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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