you can set the target label to a junk file because you won't need it.
On 4/18/2025 12:31 PM, Loïc Daumail wrote:
External Email - Use Caution
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
<dgr...@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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