Hi Doug,

I see thanks! Would --srclabel and --trglabel be identical in my case?

i.e., something like this:

freesurferCommand = f'mri_label2label --srclabel {surf_label_file} --trglabel {surf_label_file} --outmask {out_mask_file} --hemi {hID} --s {participant} --regmethod surface'

Corresponding bash code:

mri_label2label --srclabel /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 --trglabel /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 --outmask /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz --hemi lh --s sub-NSxLxYKx1964 --regmethod surface

Thanks,

Best,

-Loïc

Le ven. 18 avr. 2025 à 11:47, Douglas N. Greve <dgreve@mgh.harvard.edu> a écrit :

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:
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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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