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:
>
> 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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