Using --derivatives from Bibsnet precomputed segmentation and mask #458
Comments
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Thanks for the report - likely it's due to N4 altering the T2w's header enough to cause this mismatch. To patch this, we should preserve the original header information. |
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Thank you so much for your prompt reply! Yes, it happened to both T1w and T2w sometimes. I actually further checked the processed T1w from the inFS, and the x y z are swapped. Accordingly, when taking the segmentation from the bibsnet (it was generated as the same orientation as the original T1w), it yelled for the dimension not match. After I worked around this by manually swapped the orientation, "the affine was not similar enough", which can be worked around by copying the affine from the header as well. It is not ideal, but if this can be fixed in the next version, it would much improved the final results. Great work, thank you all so much!! |
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I have to use HPC to run this pipeline, so if there is any docker image available, I'm more than happy to try it out. Thank you so much! |
What happened?
When it started to run apply_t2w_mask after the final_clip were completed and while Loading pkl: /work/nibabies_25_1_wf/single_subject_sub-MO101_ses-0_wf/infant_anat_fit_wf/apply_t2w_mask/result_apply_t2w_mask.pklz, it raised the errors about "image size and mask size not matching". After checking the dimensions from brain masks inside the derivates created by Bibsnet, they are of the same size as the original images.
What command did you use?
What version of NiBabies are you using?
I tried the current unstable, and 25.0.1, they ended with the same errors
Relevant log output
250422-09:59:19,47 nipype.workflow WARNING: Previous output generated by version 0+unknown found. 250422-09:59:19,50 nipype.workflow IMPORTANT: Running nibabies version 25.1.0.dev7+g91c5fc3: * BIDS dataset path: /home/xna/fmri/data_M_BIDS/M_BIDS. * Participant list: [['MO101', '0']]. * Run identifier: 20250422-095900_c90c4edb-98ab-4e7f-8dbe-c8790bb15a8b. * Output spaces: MNIInfant:cohort-1:res-1 UNCInfant:cohort-1:res-native. * Derivatives: {'precomputed': PosixPath('/deriv/precomputed')}. * Pre-run FreeSurfer's SUBJECTS_DIR: /home/xna/fmri/data_M_BIDS/nibabies_out/sourcedata/freesurfer. 250422-09:59:20,65 nipype.workflow INFO: Collected the following data for sub-MO101_ses-0: Raw: {'asl': [], 'bold': ['/home/xna/fmri/data_M_BIDS/M_BIDS/sub-MO101/ses-0/func/sub-MO101_ses-0_task-rest_dir-AP_bold.nii.gz', '/home/xna/fmri/data_M_BIDS/M_BIDS/sub-MO101/ses-0/func/sub-MO101_ses-0_task-rest_dir-PA_bold.nii.gz'], 'dwi': [], 'flair': [], 'fmap': ['/home/xna/fmri/data_M_BIDS/M_BIDS/sub-MO101/ses-0/fmap/sub-MO101_ses-0_task-rest_dir-AP_epi.nii.gz', '/home/xna/fmri/data_M_BIDS/M_BIDS/sub-MO101/ses-0/fmap/sub-MO101_ses-0_task-rest_dir-PA_epi.nii.gz'], 'pet': [], 'roi': [], 'sbref': [], 't1w': ['/home/xna/fmri/data_M_BIDS/M_BIDS/sub-MO101/ses-0/anat/sub-MO101_ses-0_T1w.nii.gz'], 't2w': ['/home/xna/fmri/data_M_BIDS/M_BIDS/sub-MO101/ses-0/anat/sub-MO101_ses-0_T2w.nii.gz']} Derivatives: {'t1w_aseg': '/deriv/precomputed/sub-MO101/ses-0/anat/sub-MO101_ses-0_space-T1w_desc-aseg_dseg.nii.gz', 't1w_mask': '/deriv/precomputed/sub-MO101/ses-0/anat/sub-MO101_ses-0_space-T1w_desc-brain_mask.nii.gz', 't2w_aseg': '/deriv/precomputed/sub-MO101/ses-0/anat/sub-MO101_ses-0_space-T2w_desc-aseg_dseg.nii.gz', 't2w_mask': '/deriv/precomputed/sub-MO101/ses-0/anat/sub-MO101_ses-0_space-T2w_desc-brain_mask.nii.gz', 'transforms': {}} 250422-09:59:23,355 nipype.workflow VERBOSE: nibabies config: [environment] cpu_count = 56 exec_env = "singularity" free_mem = 81.3 overcommit_policy = "heuristic" overcommit_limit = "50%" nipype_version = "1.9.2" templateflow_version = "24.2.2" version = "25.1.0.dev7+g91c5fc3" [execution] bids_dir = "/home/xna/fmri/data_M_BIDS/M_BIDS" bids_database_dir = "/work/20250422-095900_c90c4edb-98ab-4e7f-8dbe-c8790bb15a8b/bids_db" bids_description_hash = "028f42f5696bd02de9c5cb3080bbed8b5084af6d0546cb0563298fce257924eb" boilerplate_only = false copy_derivatives = false sloppy = false debug = [] fs_license_file = "/opt/freesurfer/license.txt" fs_subjects_dir = "/home/xna/fmri/data_M_BIDS/nibabies_out/sourcedata/freesurfer" layout = "BIDS Layout: ...xna/fmri/data_M_BIDS/M_BIDS | Subjects: 1 | Sessions: 1 | Runs: 0" log_dir = "/home/xna/fmri/data_M_BIDS/nibabies_out/logs" log_level = 10 low_mem = false md_only_boilerplate = false nibabies_dir = "/home/xna/fmri/data_M_BIDS/nibabies_out" notrack = true output_dir = "/home/xna/fmri/data_M_BIDS/nibabies_out" me_output_echos = false output_layout = "bids" output_spaces = "MNIInfant:cohort-1:res-1 UNCInfant:cohort-1:res-native" reports_only = false run_uuid = "20250422-095900_c90c4edb-98ab-4e7f-8dbe-c8790bb15a8b" session_id = [ "0",] participant_label = [ "MO101",] templateflow_home = "/home/nibabies/.cache/templateflow" unique_labels = [ [ "MO101", "0",],] work_dir = "/work" write_graph = false [workflow] analysis_level = "participant" anat_only = true bold2anat_dof = 6 bold2anat_init = "auto" cifti_output = false fd_radius = 45 fmap_bspline = false force_syn = false hires = true hmc_bold_frame = 16 ignore = [] level = "full" longitudinal = false medial_surface_nan = false multi_step_reg = false norm_csf = false project_goodvoxels = false regressors_all_comps = false regressors_dvars_th = 1.5 regressors_fd_th = 0.5 run_reconall = true skull_strip_fixed_seed = false skull_strip_template = "UNCInfant:cohort-1" skull_strip_anat = "force" slice_time_ref = 0.5 surface_recon_method = "infantfs" use_bbr = false use_syn_sdc = false me_t2s_fit_method = "curvefit" [nipype] crashfile_format = "txt" get_linked_libs = false nprocs = 56 omp_nthreads = 8 plugin = "MultiProc" resource_monitor = false stop_on_first_crash = true [seeds] master = 47313 ants = 16994 numpy = 41834 [execution.dataset_links] raw = "/home/xna/fmri/data_M_BIDS/M_BIDS" templateflow = "/home/nibabies/.cache/templateflow" precomputed = "/deriv/precomputed" [execution.derivatives] precomputed = "/deriv/precomputed" [nipype.plugin_args] maxtasksperchild = 1 raise_insufficient = false 250422-10:28:37,240 nipype.workflow INFO: [Job 56] Completed (nibabies_25_1_wf.single_subject_sub-MO101_ses-0_wf.infant_anat_fit_wf.t1w_n4_wf.final_clip). 250422-10:28:37,241 nipype.workflow DEBUG: Clearing 66 from queue 250422-10:28:37,242 nipype.utils DEBUG: Loading pkl: /work/nibabies_25_1_wf/single_subject_sub-MO101_ses-0_wf/infant_anat_fit_wf/apply_t2w_mask/result_apply_t2w_mask.pklz 250422-10:28:37,242 nipype.workflow ERROR: Node apply_t2w_mask failed to run on host xbt085. 250422-10:28:37,243 nipype.workflow ERROR: Saving crash info to /home/xna/fmri/data_M_BIDS/nibabies_out/sub-MO101/ses-0/log/20250422-095900_c90c4edb-98ab-4e7f-8dbe-c8790bb15a8b/crash-20250422-102837-xna-apply_t2w_mask-4bd297b5-362b-4dff-94e8-9e0562bbae51.txt Traceback (most recent call last): File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node result["result"] = node.run(updatehash=updatehash) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run result = self._run_interface(execute=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface return self._run_command(execute) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node apply_t2w_mask. Traceback: Traceback (most recent call last): File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 401, in run runtime = self._run_interface(runtime) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/niworkflows/interfaces/nibabel.py", line 73, in _run_interface raise ValueError('Image and mask sizes do not match.') ValueError: Image and mask sizes do not match. 250422-10:28:37,243 nipype.workflow INFO: [Node] Setting-up "nibabies_25_1_wf.single_subject_sub-MO101_ses-0_wf.infant_anat_fit_wf.coregistration_wf.coreg" in "/work/nibabies_25_1_wf/single_subject_sub-MO101_ses-0_wf/infant_anat_fit_wf/coregistration_wf/coreg". 250422-10:28:37,244 nipype.workflow CRITICAL: nibabies failed: Traceback (most recent call last): File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node result["result"] = node.run(updatehash=updatehash) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run result = self._run_interface(execute=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface return self._run_command(execute) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node apply_t2w_mask. Traceback: Traceback (most recent call last): File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 401, in run runtime = self._run_interface(runtime) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/niworkflows/interfaces/nibabel.py", line 73, in _run_interface raise ValueError('Image and mask sizes do not match.') ValueError: Image and mask sizes do not match. 250422-10:28:37,258 nipype.workflow INFO: [Node] Executing "coreg" <niworkflows.interfaces.fixes.FixHeaderRegistration> Traceback (most recent call last): File "/opt/conda/envs/nibabies/bin/nibabies", line 8, in <module> sys.exit(main()) ^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/run.py", line 104, in main nibabies_wf.run(**_plugin) File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/workflows.py", line 625, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/base.py", line 177, in run self._clean_queue(jobid, graph, result=result) File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/base.py", line 255, in _clean_queue raise RuntimeError("".join(result["traceback"])) RuntimeError: Traceback (most recent call last): File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node result["result"] = node.run(updatehash=updatehash) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run result = self._run_interface(execute=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface return self._run_command(execute) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node apply_t2w_mask. Traceback: Traceback (most recent call last): File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 401, in run runtime = self._run_interface(runtime) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/niworkflows/interfaces/nibabel.py", line 73, in _run_interface raise ValueError('Image and mask sizes do not match.') ValueError: Image and mask sizes do not match.Add any additional information or context about the problem here.
No response
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