Summary of what happened:
I am running Amico reconstruction using the following command and it failed.
Command used (and if a helper script was used, a link to the helper script or the command generated):
/bin/singularity run --containall --writable-tmpfs \
-B $HOME,/home,/net,/onrc,{analysisrootdir}/sourcedata,{analysisrootdir}/sourcedata/Results,{analysisrootdir}/tmp,${FREESURFER_HOME}/license.txt:/opt/freesurfer-7.4.1/license.txt \
/home/Amubeen/onrc/data/NODDI/qsiprep/qsiprep-0.22.0.sif \
{analysisrootdir}/sourcedata {analysisrootdir}/sourcedata/Results participant \
-w {analysisrootdir}/tmp \
--output-resolution 1.2 \
--participant_label sub-{subjectuid} \
--recon-spec amico_noddi \
--recon-input /home/pipeline/onrc/data2/pipelineb/NODDIPreprocessing/{subjectuid}/{studynum}/sourcedata/Results/qsiprep \
--fs-license-file /opt/freesurfer-7.4.1/license.txt
Version:
0.22.1
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
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):
250123-13:04:39,800 nipype.workflow INFO:
Running recon-only mode: --recon-input was used.
250123-13:04:39,802 nipype.workflow IMPORTANT:
Running QSIRecon version 0.22.1.dev0+gd9279db.d20240719
License NOTICE ##################################################
QSIPrep 0.22.1.dev0+gd9279db.d20240719
Copyright The PennLINC Developers.
This product includes software developed by
the NiPreps Community (https://nipreps.org/).
Portions of this software were developed at the Department of
Psychology at Stanford University, Stanford, CA, US.
This software is also distributed as a Docker container image.
The bootstrapping file for the image ("Dockerfile") is licensed
under the MIT License.
This software may be distributed through an add-on package called
"Docker Wrapper" that is under the BSD 3-clause License.
#################################################################
250123-13:04:39,856 nipype.workflow IMPORTANT:
Building QSIRecon's workflow:
* BIDS dataset path: /home/pipeline/onrc/data2/pipelineb/NODDIAmico/S6009NYC/5/sourcedata.
* Participant list: ['S6009NYC'].
* Run identifier: 20250123-130428_d582b8a4-7169-48a0-bc27-7ce5e4ad49ff.
250123-13:04:39,984 nipype.workflow INFO:
found ['/home/pipeline/onrc/data2/pipelineb/NODDIPreprocessing/S6009NYC/5/sourcedata/Results/qsiprep/sub-S6009NYC/ses-5/dwi/sub-S6009NYC_ses-5_acq-diffAPMPoptMB450b100050b20008b0lowflip_space-T1w_desc-preproc_dwi.nii.gz'] in /home/pipeline/onrc/data2/pipelineb/NODDIPreprocessing/S6009NYC/5/sourcedata/Results/qsiprep
250123-13:04:39,985 nipype.workflow INFO:
CHECKING /home/pipeline/onrc/data2/pipelineb/NODDIPreprocessing/S6009NYC/5/sourcedata/Results/qsiprep/sub-S6009NYC/anat/sub-S6009NYC_desc-brain_mask.nii.gz: True
250123-13:04:39,985 nipype.workflow INFO:
CHECKING /home/pipeline/onrc/data2/pipelineb/NODDIPreprocessing/S6009NYC/5/sourcedata/Results/qsiprep/sub-S6009NYC/anat/sub-S6009NYC_desc-preproc_T1w.nii.gz: True
250123-13:04:39,985 nipype.workflow INFO:
Found usable QSIPrep-preprocessed T1w image and mask.
250123-13:04:39,986 nipype.workflow INFO:
CHECKING /home/pipeline/onrc/data2/pipelineb/NODDIPreprocessing/S6009NYC/5/sourcedata/Results/qsiprep/sub-S6009NYC/anat/sub-S6009NYC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5: True
250123-13:04:39,986 nipype.workflow INFO:
CHECKING /home/pipeline/onrc/data2/pipelineb/NODDIPreprocessing/S6009NYC/5/sourcedata/Results/qsiprep/sub-S6009NYC/anat/sub-S6009NYC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5: True
250123-13:04:39,986 nipype.workflow INFO:
Found high-res anatomical data in preprocessed inputs for S6009NYC.
250123-13:04:39,987 nipype.workflow INFO:
Anatomical (T1w) available for recon: {'has_qsiprep_5tt_hsvs': False, 'has_freesurfer_5tt_hsvs': False, 'has_freesurfer': False, 'has_qsiprep_t1w': True, 'has_qsiprep_t1w_transforms': True}
[{'bids_dwi_file': '/home/pipeline/onrc/data2/pipelineb/NODDIPreprocessing/S6009NYC/5/sourcedata/Results/qsiprep/sub-S6009NYC/ses-5/dwi/sub-S6009NYC_ses-5_acq-diffAPMPoptMB450b100050b20008b0lowflip_space-T1w_desc-preproc_dwi.nii.gz'}]
{'has_qsiprep_5tt_hsvs': False, 'has_freesurfer_5tt_hsvs': False, 'has_freesurfer': False, 'has_qsiprep_t1w': True, 'has_qsiprep_t1w_transforms': True}
250123-13:04:39,993 nipype.workflow INFO:
Transforming ODF ROIs into DWI space for visual report.
250123-13:04:41,991 nipype.workflow INFO:
QSIRecon workflow graph with 28 nodes built successfully.
250123-13:04:53,301 nipype.workflow IMPORTANT:
QSIRecon started!
250123-13:04:58,910 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.recon_anatomical_wf.qsiprep_anat_ingress" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/recon_anatomical_wf/qsiprep_anat_ingress".
250123-13:04:58,921 nipype.workflow INFO:
[Node] Executing "qsiprep_anat_ingress"
250123-13:04:58,930 nipype.workflow INFO:
[Node] Finished "qsiprep_anat_ingress", elapsed time 0.007085s.
250123-13:04:59,2 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_ingressed_dwi_data" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_ingressed_dwi_data".
250123-13:04:59,10 nipype.workflow INFO:
[Node] Executing "sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_ingressed_dwi_data"
250123-13:04:59,15 nipype.workflow INFO:
[Node] Finished "sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_ingressed_dwi_data", elapsed time 0.003493s.
250123-13:04:59,523 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf.output_grid_wf.voxel_size_chooser" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf/output_grid_wf/voxel_size_chooser".
250123-13:04:59,524 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf.resample_mask" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf/resample_mask".
250123-13:04:59,563 nipype.workflow INFO:
[Node] Executing "resample_mask"
250123-13:04:59,566 nipype.workflow INFO:
[Node] Executing "voxel_size_chooser"
250123-13:04:59,567 nipype.workflow INFO:
[Node] Finished "voxel_size_chooser", elapsed time 0.000133s.
250123-13:04:59,575 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf.odf_rois" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf/odf_rois".
250123-13:04:59,588 nipype.workflow INFO:
[Node] Executing "odf_rois"
250123-13:05:01,304 nipype.workflow INFO:
[Node] Finished "resample_mask", elapsed time 1.185819s.
250123-13:05:01,313 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf.output_grid_wf.autobox_template" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf/output_grid_wf/autobox_template".
250123-13:05:01,323 nipype.workflow INFO:
[Node] Executing "autobox_template"
250123-13:05:04,178 nipype.workflow INFO:
[Node] Finished "autobox_template", elapsed time 2.853759s.
250123-13:05:05,523 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf.output_grid_wf.deoblique_autobox" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf/output_grid_wf/deoblique_autobox".
250123-13:05:05,534 nipype.workflow INFO:
[Node] Executing "deoblique_autobox"
250123-13:05:06,726 nipype.workflow INFO:
[Node] Finished "deoblique_autobox", elapsed time 1.190776s.
250123-13:05:07,567 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf.output_grid_wf.resample_to_voxel_size" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_dwi_specific_anat_wf/output_grid_wf/resample_to_voxel_size".
250123-13:05:09,963 nipype.workflow INFO:
[Node] Executing "resample_to_voxel_size"
250123-13:05:10,614 nipype.workflow INFO:
[Node] Finished "resample_to_voxel_size", elapsed time 0.648789s.
250123-13:05:30,196 nipype.workflow INFO:
[Node] Finished "odf_rois", elapsed time 30.065785s.
250123-13:05:33,344 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_inputs" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_inputs".
250123-13:05:33,366 nipype.workflow INFO:
[Node] Executing "sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_inputs"
250123-13:05:33,369 nipype.workflow INFO:
[Node] Finished "sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_inputs", elapsed time 0.000361s.
250123-13:05:33,534 nipype.workflow INFO:
[Node] Setting-up "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_wf.fit_noddi.recon_noddi" in "/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_wf/fit_noddi/recon_noddi".
250123-13:05:33,549 nipype.workflow INFO:
[Node] Executing "recon_noddi"
-> Rounding b-values to nearest multiple of 50.0
-> Writing scheme file to [ /net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_wf/fit_noddi/recon_noddi/study/subject/sub-S6009NYC_ses-5_acq-diffAPMPoptMB450b100050b20008b0lowflip_space-T1w_desc-preproc_dwi.scheme ]
e[0;32m
-> Loading data:e[0m
* DWI signal
- dim = 134 x 165 x 142 x 100
- pixdim = 1.200 x 1.200 x 1.200
* Acquisition scheme
- 100 samples, 2 shells
- 7 @ b=0 , 47 @ b=1000.0 , 46 @ b=2000.0
* Binary mask
- dim = 134 x 165 x 142
- pixdim = 1.200 x 1.200 x 1.200
- voxels = 836823
e[0;32m [ 7.2 seconds ]e[0m
e[0;32m
-> Preprocessing:e[0m
* Normalizing to b0... [ min=0.00, mean=0.51, max=18.15 ]
* Keeping all b0 volume(s)
e[0;32m [ 1.7 seconds ]e[0m
250123-13:05:42,515 nipype.interface INFO:
Fitting NODDI Model.
e[0;32m
-> Creating LUT for "NODDI" model:e[0m
e[0;30;41m[ ERROR ]e[0;31m Auxiliary matrices not found; call "amico.setup()" firste[0m
250123-13:05:42,749 nipype.workflow INFO:
[Node] Finished "recon_noddi", elapsed time 8.96873s.
250123-13:05:42,749 nipype.workflow WARNING:
Storing result file without outputs
250123-13:05:42,752 nipype.workflow WARNING:
[Node] Error on "qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_wf.fit_noddi.recon_noddi" (/net/hhctnas01/mnt/pool1/home/home/pipeline/data/pipelineb/NODDIAmico/S6009NYC/5/tmp/qsirecon_0_22_wf/sub-S6009NYC_amico_noddi/sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_wf/fit_noddi/recon_noddi)
250123-13:05:43,421 nipype.workflow ERROR:
Node recon_noddi failed to run on host humboldt.
250123-13:05:43,429 nipype.workflow ERROR:
Saving crash info to /home/pipeline/onrc/data2/pipelineb/NODDIAmico/S6009NYC/5/sourcedata/Results/qsirecon/sub-S6009NYC/log/20250123-130428_d582b8a4-7169-48a0-bc27-7ce5e4ad49ff/crash-20250123-130543-nidb-recon_noddi-dc3cfa44-3241-4b01-85b4-7e8a35c9da33.txt
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node recon_noddi.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/amico.py", line 188, in _run_interface
aeval.generate_kernels()
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/amico/core.py", line 362, in generate_kernels
aux = amico.lut.load_precomputed_rotation_matrices( lmax, ndirs )
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/amico/lut.py", line 153, in load_precomputed_rotation_matrices
ERROR( 'Auxiliary matrices not found; call "amico.setup()" first' )
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/amico/util.py", line 49, in ERROR
exit(EX_USAGE)
SystemExit: 64
250123-13:05:45,421 nipype.workflow ERROR:
could not run node: qsirecon_0_22_wf.sub-S6009NYC_amico_noddi.sub_S6009NYC_ses_5_acq_diffAPMPoptMB450b100050b20008b0lowflip_space_T1w_desc_preproc_recon_wf.fit_noddi.recon_noddi
250123-13:05:45,487 nipype.workflow CRITICAL:
QSIRecon failed: Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node recon_noddi.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/amico.py", line 188, in _run_interface
aeval.generate_kernels()
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/amico/core.py", line 362, in generate_kernels
aux = amico.lut.load_precomputed_rotation_matrices( lmax, ndirs )
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/amico/lut.py", line 153, in load_precomputed_rotation_matrices
ERROR( 'Auxiliary matrices not found; call "amico.setup()" first' )
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/amico/util.py", line 49, in ERROR
exit(EX_USAGE)
SystemExit: 64