Help with freesurfer's mri_label2vol

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1

Greetings,

I’m trying to learn about the freesurfer files produced by my fmriprep v20.2.7 pipeline.
My goal is to use the perirhinal label file generated by freesurfer and turn it into a native space binary mask.

My searches lead me to use mri_label2vol - Free Surfer Wiki function to transform my perirhinal_exvivo.thresh.label files to volumes.

import subprocess

# Define the subject's directory

SUBJECTS_DIR="/xxx/xxx/xxx/xxx/bids/derivatives/fmriprep-20.2.7"

# Define the subject ID

SUBJECT_ID="sub-xxx"

# Define the label paths

label_path_left = f"{SUBJECTS_DIR}/freesurfer/{SUBJECT_ID}/label/lh.perirhinal_exvivo.thresh.label"

label_path_right = f"{SUBJECTS_DIR}/freesurfer/{SUBJECT_ID}/label/rh.perirhinal_exvivo.thresh.label"

template_path = f"{SUBJECTS_DIR}/fmriprep/{SUBJECT_ID}/anat/{SUBJECT_ID}_desc-preproc_T1w.nii.gz"

# Define the output paths for the binary volume masks

output_path_left = f"{SUBJECTS_DIR}/freesurfer/{SUBJECT_ID}/mri/lh.perirhinal_exvivo.thresh.mask.nii.gz"

output_path_right = f"{SUBJECTS_DIR}/freesurfer/{SUBJECT_ID}/mri/rh.perirhinal_exvivo.thresh.mask.nii.gz"

# Convert the left hemisphere label to a binary volume mask

subprocess.run(["mri_label2vol", "--label", label_path_left, "--temp", template_path, "--subject", SUBJECT_ID, "--hemi", "lh", "--identity", "--fillthresh", "0.5", "--o", output_path_left], check=True)

# Convert the left hemisphere label to a binary volume mask

subprocess.run(["mri_label2vol", "--label", label_path_right, "--temp", template_path, "--subject", SUBJECT_ID, "--hemi", "rh", "--identity", "--fillthresh", "0.5", "--o", output_path_right], check=True)

from nilearn import plotting

plotting.plot_roi(output_path_left, bg_img=template_path, cmap="Set1", draw_cross=False)

plotting.plot_roi(output_path_right, bg_img=template_path, cmap="Set1", draw_cross=False)

however when I plot this mask, it doesn’t seem to be in the right place

image

I’m guessing that I’m missing --reg regmatfile parameter, but I don’t know which file that would be…

1 Like
2

You probably want --regheader, not --identity.

3

Thanks,

–regheader on its own produces an error

 subprocess.run(["mri_label2vol", "--label", label_path_right, "--temp", template_path, "--subject", SUBJECT_ID, "--hemi", "rh", "--regheader",  "--fillthresh", "0.5", "--o", output_path_right], check=True)
ERROR: --regheader requires one argument unless you
are going to use a --seg. If so specify that before --regheader

…but providing an orig.mgz it works?

regheader_path = f"{SUBJECTS_DIR}/freesurfer/{SUBJECT_ID}/mri/orig.mgz"

subprocess.run(["mri_label2vol", "--label", label_path_left, "--temp", template_path, "--subject", SUBJECT_ID, "--hemi", "lh", "--regheader", regheader_path,  "--fillthresh", "0.5", "--o", output_path_left], check=True)

is this correct? There is not much documentation on this flag for mri_label2vol

4

Seems like it should be fine. Does the output look reasonable?

5

Yes, its spot on, thanks!