📋 C-PAC v1.7.0 ― brainlife: Try with `--preconfig anat-only`

[shnizzedy]

C-PAC Run Info

Description	attempting to run C-PAC on brainlife with --preconfig anat-only
Version	v1.7.0
Container	Singularity
System	brainlife
Data Size	176 × 256 × 256
Results	completed successfully

Include:

• [x] Run Command:

time singularity run -e -B $PWD/tmp:/tmp cpac-singularity-image.simg bids output participant --preconfig anat-only --save_working_dir

• [x] Pipeline Config: anat-only.yml
• [ ] Data Config: BIDS directory
• [x] Screenshots of brain extraction and registration wireframe overlays from QC pages (if available):

• [x] Node timing information:

('resting_preproc_sub-A00021039_ses-DS2.anat_mni_ants_register_0.calc_ants_warp', 1719.0)

('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_afni_0.anat_n4', 1434.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.segment', 259.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_afni_0.anat_skullstrip', 102.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_skullstrip_0.skull_edge', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.montage_s', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.montage_a', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_afni_0.anat_deoblique', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_afni_0.anat_reorient', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_skullstrip_0.montage_skull.resample_o', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_afni_0.anat_brain_mask', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_afni_0.anat_skullstrip_orig_vol', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.GM.overlap_GM_map_with_prior', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.WM_prior_mni_to_t1', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.CSF.overlap_CSF_map_with_prior', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_afni_0.anat_skullstrip_args', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.resample_u', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_skullstrip_0.montage_skull.resample_u', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.check_for_s3_PRIORS_WHITE', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_anatomical_to_standard', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_mni_ants_register_0.select_forward_warp', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_ants_affine_xfm', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_mni_ants_register_0.select_forward_initial', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.GM.GM_inverse_transform_flags', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.GM.GM_prior_mni_to_t1', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.GM.binarize_GM', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.resample_o_gm', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.WM_collect_linear_transforms', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.overlap_WM_map_with_prior', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.binarize_WM', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.resample_o_wm', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_anatomical_wm_mask', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.CSF.CSF_inverse_transform_flags', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.CSF.CSF_prior_mni_to_t1', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.CSF.binarize_CSF', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.resample_o_csf', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_qc_csf_gm_wm_s', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_template_edge_0', 1.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_gather_0.check_for_s3', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_anatomical_reorient', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_qc_skullstrip_vis_s', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0qcskullstrip_vis_a', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_anatomical_brain', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.check_for_s3_PRIORS_GRAY', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.check_for_s3_PRIORS_CSF', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.resampled_template_skull_for_anat', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.resampled_template_brain_for_anat', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_mni_anat_0.resample_u', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_mni_ants_register_0.select_inverse_warp', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_mni_to_anatomical_nonlinear_xfm', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_anatomical_to_mni_nonlinear_xfm', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_mni_ants_register_0.select_forward_affine', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_mni_ants_register_0.select_forward_rigid', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_ants_rigid_xfm', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.GM.GM_collect_linear_transforms', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.GM.GM_check_transforms', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_anatomical_gm_mask', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.WM_check_transforms', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.WM_inverse_transform_flags', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.CSF.CSF_collect_linear_transforms', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.CSF.CSF_check_transforms', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0qccsf_gm_wm_a', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_anatomical_csf_mask', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_ants_initial_xfm', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_mni_anat_0.resample_o', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_qc_mni_normalized_anatomical_s', 0.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0qcmni_normalized_anatomical_a', 0.0) |