Summary of what happened:
Hi neurostars,
I’m new to this list, and I’m trying to run nibabies on a segmentation for a six-month old baby that was generated by a third-party organization (probably before nibabies/bibsnet existed). The GM/WM boundary looks surprising good, despite the age. I am trying to fool nibabies into believing it is bibsnet-generated, so I relabeled the ROI’s to match FreeSurferColorLUT.txt ( freesurfer/distribution/FreeSurferColorLUT.txt at dev · freesurfer/freesurfer · GitHub ). There were a few ROI’s missing, including Left/Right-Accumbens-area.
You can see my errors below.
There is a nibabies-generated label table here:
nibabies_25_2_wf/single_subject_sub-103840_ses-6mo_wf/bold_ses_6mo_task_rest_run_01_wf/subcortical_mni_alignment_wf/atlas_labels/tpl-MNI152NLin6Asym_res-02_atlas-HCP_dseg_labels.txt
If I’m reading it correctly, vol0009 corresponds to DIENCEPHALON_VENTRAL_LEFT.
It’s true that my third-party segmentation is missing this label, but so are other bibsnet-generated segmentations I have looked at that process through nibabies successfully.
Any ideas of what I can do to get past this? These third-party segmentations look promising, especially for this age group.
Thanks,
Donna
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run --rm -i -u XXXX:YY \
-v /my_fs_distro/.license:/opt/freesurfer/license.txt:ro \
-v /my/dataset/folder/rawdata:/data:ro \
-v /my/dataset/folder/derivatives/nibabies:/out \
-v /my/dataset/folder/work/nibabies/sub-103840:/work \
-v /my/dataset/folder/derivatives/bibsnet:/deriv1 \
nipreps/nibabies:25.2.1 \
/data /out participant \
--participant-label 103840 \
-s 6mo \
-w /work \
--verbose \
--derivatives /deriv1 \
--fd-spike-threshold 0.2 \
--age-months 6 \
--surface-recon-method infantfs \
--cifti-output 91k \
--debug registration \
--project-goodvoxels \
--multi-step-reg \
--norm-csf \
--omp-nthreads 7 --mem 100G --nprocs 7 \
--stop-on-first-crash \
--output-spaces fsLR MNIInfant:cohort-3 MNI152NLin6Asym:res-2 T1w
Version:
nipreps/nibabies:25.2.1
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
I was getting this error:
WARNING: Failed to parse caret volume extension: unexpected character
line number: 39 column number: 1
While running:
wb_command -cifti-create-dense-timeseries out.dtseries.nii -volume /work/nibabies_25_2_wf/single_subject_sub-103840_ses-6mo_wf/bold_ses_6mo_task_rest_run_01_wf/subcortical_mni_alignment_wf/bold_mask_roi/mapflow/_bold_mask_roi8/sub-103840_ses-6mo_task-rest_run-01_bold_valid_tshift_xformresampled_flirt_masked.nii.gz /work/nibabies_25_2_wf/single_subject_sub-103840_ses-6mo_wf/bold_ses_6mo_task_rest_run_01_wf/subcortical_mni_alignment_wf/vol_label/mapflow/_vol_label8/vol0008_flirt_maths_labels.nii.gz
ERROR: cifti xml dimensions must be greater than zero
So I drew in the accumbens and it got a step further. Now it fails with:
WARNING: Failed to parse caret volume extension: unexpected character
line number: 39 column number: 1
While running:
wb_command -cifti-create-dense-timeseries out.dtseries.nii -volume /work/nibabies_25_2_wf/single_subject_sub-103840_ses-6mo_wf/bold_ses_6mo_task_rest_run_01_wf/subcortical_mni_alignment_wf/bold_mask_roi/mapflow/_bold_mask_roi9/sub-103840_ses-6mo_task-rest_run-01_bold_valid_tshift_xformresampled_flirt_masked.nii.gz /work/nibabies_25_2_wf/single_subject_sub-103840_ses-6mo_wf/bold_ses_6mo_task_rest_run_01_wf/subcortical_mni_alignment_wf/vol_label/mapflow/_vol_label9/vol0009_flirt_maths_labels.nii.gz
ERROR: cifti xml dimensions must be greater than zero