surf2vol does not take labels as an input. Instead, use mri_label2label
to convert it to a mask, then use mri_surf2vol on the mask
On 4/18/2025 11:39 AM, Loïc Daumail wrote:
External Email - Use Caution
Dear all,
I am trying to convert label files into volume ROI masks.
This is my command below:
mri_surf2vol --surfval
/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label
--o
/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/fonctional_vol_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz
--identity sub-NSxLxYKx1964 --hemi lh --fillribbon --template
/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/mri/brain.mgz
I get this error:
Reading surface
/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.white
Done reading source surface
Reading thickness
/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.thickness
Done
INFO:
reading/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label
as unknown
mri_read(): type = 32
error: mri_read(): code inconsistency (file type recognized but not
caught)
ERROR: could not read
/Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label
as unknown
Any idea what would cause this? Is it because the labels weren't saved
in the correct format?
Thanks,
Best,
-Loïc
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