[Neuroimaging] nipype pipeline crashes at final step due to pathing issues
Boulakis Paradeisios
Paradeisios.Boulakis at uliege.be
Sat Apr 13 09:12:57 EDT 2024
Hello everyone, I have the following pipeline.
# %%
infosource = Node(IdentityInterface(fields="subject_list"]), name="infosource")
infosource.iterables = [("subject_list", subject_list)]
templates = {
"mask": "{subject_list}/func/{subject_list}_task-gonogo_run-{run_list}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz",
"func": "{subject_list}/func/{subject_list}_task-gonogo_run-{run_list}_*_desc-smooth+preproc_bold.nii.gz",
"confounds": "{subject_list}/func/{subject_list}_task-gonogo_run-{run_list}_desc-confounds_timeseries.tsv",
}
selectfiles = MapNode(
SelectFiles(templates), name="selectfiles", iterfield=["run_list"]
)
selectfiles.inputs.base_directory = res_dir
selectfiles.inputs.run_list = run_list
sink = Node(DataSink(), name="sink")
sink.inputs.base_directory = str(res_dir)
# %%
desmat = MapNode(
Function(
input_names=["confounds", "res_dir", "gs"],
output_names=["confound_txt"],
function=filter_confound_file,
),
name="desmat",
iterfield=["confounds"],
)
desmat.inputs.res_dir = res_dir
desmat.inputs.gs = False
glm = MapNode(GLM(), name="glm", iterfield=["design", "in_file", "mask"])
glm.inputs.out_res_name = "glm_residuals.nii"
glm.inputs.out_file = "glm.nii"
glm.inputs.output_type = "NIFTI"
glm.inputs.demean = False
# Bandpass Filtering
bpf = MapNode(Bandpass(), name="bpf", iterfield=["in_file"])
bpf.inputs.lowpass = 0.09
bpf.inputs.highpass = 0.008
bpf.inputs.tr = TR
bpf.inputs.out_file = "bpf_filt"
# %%
den_workflow = Workflow(name="den_workflow")
den_workflow.base_dir = str(res_dir)
den_workflow.connect(infosource, "subject_list", selectfiles, "subject_list")
den_workflow.connect(selectfiles, "confounds", desmat, "confounds")
den_workflow.connect(selectfiles, "func", glm, "in_file")
den_workflow.connect(selectfiles, "mask", glm, "mask")
den_workflow.connect(desmat, "confound_txt", glm, "design")
den_workflow.connect(glm, "out_res", bpf, "in_file")
den_workflow.connect(glm, "out_res", sink, "glm. at out_res")
den_workflow.connect(glm, "out_file", sink, "glm. at out_file")
den_workflow.connect(bpf, "out_file", sink, "bpf. at bpf_filt")
For every of the four runs that I feed in the pipeline, I get the following error
240412-23:41:13,610 nipype.workflow INFO:
Workflow den_workflow settings: ['check', 'execution', 'logging', 'monitoring']
240412-23:41:13,621 nipype.workflow INFO:
Running in parallel.
240412-23:41:13,659 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:41:15,663 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:41:15,777 nipype.workflow INFO:
[Node] Setting-up "_selectfiles0" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/selectfiles/mapflow/_selectfiles0".
240412-23:41:15,779 nipype.workflow INFO:
[Node] Setting-up "_selectfiles2" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/selectfiles/mapflow/_selectfiles2".
240412-23:41:15,778 nipype.workflow INFO:
[Node] Setting-up "_selectfiles1" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/selectfiles/mapflow/_selectfiles1".
240412-23:41:15,780 nipype.workflow INFO:
[Node] Setting-up "_selectfiles3" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/selectfiles/mapflow/_selectfiles3".
240412-23:41:15,788 nipype.workflow INFO:
[Node] Executing "_selectfiles0" <nipype.interfaces.io.SelectFiles>
240412-23:41:15,789 nipype.workflow INFO:
[Node] Executing "_selectfiles1" <nipype.interfaces.io.SelectFiles>
240412-23:41:15,790 nipype.workflow INFO:
[Node] Executing "_selectfiles2" <nipype.interfaces.io.SelectFiles>
240412-23:41:15,791 nipype.workflow INFO:
[Node] Executing "_selectfiles3" <nipype.interfaces.io.SelectFiles>
240412-23:41:15,795 nipype.workflow INFO:
[Node] Finished "_selectfiles0", elapsed time 0.0027s.
240412-23:41:15,796 nipype.workflow INFO:
[Node] Finished "_selectfiles1", elapsed time 0.002676s.
240412-23:41:15,796 nipype.workflow INFO:
[Node] Finished "_selectfiles2", elapsed time 0.002495s.
240412-23:41:15,797 nipype.workflow INFO:
[Node] Finished "_selectfiles3", elapsed time 0.002494s.
240412-23:41:17,666 nipype.workflow INFO:
[Job 5] Completed (_selectfiles0).
240412-23:41:17,670 nipype.workflow INFO:
[Job 6] Completed (_selectfiles1).
240412-23:41:17,672 nipype.workflow INFO:
[Job 7] Completed (_selectfiles2).
240412-23:41:17,674 nipype.workflow INFO:
[Job 8] Completed (_selectfiles3).
240412-23:41:17,677 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:41:17,785 nipype.workflow INFO:
[Node] Setting-up "_selectfiles0" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/selectfiles/mapflow/_selectfiles0".
240412-23:41:17,792 nipype.workflow INFO:
[Node] Executing "_selectfiles0" <nipype.interfaces.io.SelectFiles>
240412-23:41:17,796 nipype.workflow INFO:
[Node] Finished "_selectfiles0", elapsed time 0.001777s.
240412-23:41:17,801 nipype.workflow INFO:
[Node] Setting-up "_selectfiles1" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/selectfiles/mapflow/_selectfiles1".
240412-23:41:17,804 nipype.workflow INFO:
[Node] Executing "_selectfiles1" <nipype.interfaces.io.SelectFiles>
240412-23:41:17,806 nipype.workflow INFO:
[Node] Finished "_selectfiles1", elapsed time 0.000648s.
240412-23:41:17,809 nipype.workflow INFO:
[Node] Setting-up "_selectfiles2" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/selectfiles/mapflow/_selectfiles2".
240412-23:41:17,812 nipype.workflow INFO:
[Node] Executing "_selectfiles2" <nipype.interfaces.io.SelectFiles>
240412-23:41:17,814 nipype.workflow INFO:
[Node] Finished "_selectfiles2", elapsed time 0.000631s.
240412-23:41:17,817 nipype.workflow INFO:
[Node] Setting-up "_selectfiles3" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/selectfiles/mapflow/_selectfiles3".
240412-23:41:17,819 nipype.workflow INFO:
[Node] Executing "_selectfiles3" <nipype.interfaces.io.SelectFiles>
240412-23:41:17,821 nipype.workflow INFO:
[Node] Finished "_selectfiles3", elapsed time 0.0007s.
240412-23:41:19,666 nipype.workflow INFO:
[Job 0] Completed (den_workflow.selectfiles).
240412-23:41:19,671 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:41:21,669 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:41:21,732 nipype.workflow INFO:
[Node] Setting-up "_desmat3" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/desmat/mapflow/_desmat3".
240412-23:41:21,732 nipype.workflow INFO:
[Node] Setting-up "_desmat0" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/desmat/mapflow/_desmat0".
240412-23:41:21,733 nipype.workflow INFO:
[Node] Setting-up "_desmat1" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/desmat/mapflow/_desmat1".
240412-23:41:21,733 nipype.workflow INFO:
[Node] Setting-up "_desmat2" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/desmat/mapflow/_desmat2".
240412-23:41:21,738 nipype.workflow INFO:
[Node] Executing "_desmat3" <nipype.interfaces.utility.wrappers.Function>
240412-23:41:21,744 nipype.workflow INFO:
[Node] Executing "_desmat1" <nipype.interfaces.utility.wrappers.Function>
240412-23:41:21,744 nipype.workflow INFO:
[Node] Executing "_desmat0" <nipype.interfaces.utility.wrappers.Function>
240412-23:41:21,744 nipype.workflow INFO:
[Node] Executing "_desmat2" <nipype.interfaces.utility.wrappers.Function>
240412-23:41:21,822 nipype.workflow INFO:
[Node] Finished "_desmat2", elapsed time 0.07478s.
240412-23:41:21,828 nipype.workflow INFO:
[Node] Finished "_desmat0", elapsed time 0.080424s.
240412-23:41:21,829 nipype.workflow INFO:
[Node] Finished "_desmat3", elapsed time 0.088039s.
240412-23:41:21,844 nipype.workflow INFO:
[Node] Finished "_desmat1", elapsed time 0.096595s.
240412-23:41:23,670 nipype.workflow INFO:
[Job 9] Completed (_desmat0).
240412-23:41:23,673 nipype.workflow INFO:
[Job 10] Completed (_desmat1).
240412-23:41:23,675 nipype.workflow INFO:
[Job 11] Completed (_desmat2).
240412-23:41:23,677 nipype.workflow INFO:
[Job 12] Completed (_desmat3).
240412-23:41:23,680 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:41:23,757 nipype.workflow INFO:
[Node] Setting-up "_desmat0" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/desmat/mapflow/_desmat0".
240412-23:41:23,760 nipype.workflow INFO:
[Node] Cached "_desmat0" - collecting precomputed outputs
240412-23:41:23,762 nipype.workflow INFO:
[Node] "_desmat0" found cached.
240412-23:41:23,764 nipype.workflow INFO:
[Node] Setting-up "_desmat1" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/desmat/mapflow/_desmat1".
240412-23:41:23,766 nipype.workflow INFO:
[Node] Cached "_desmat1" - collecting precomputed outputs
240412-23:41:23,767 nipype.workflow INFO:
[Node] "_desmat1" found cached.
240412-23:41:23,769 nipype.workflow INFO:
[Node] Setting-up "_desmat2" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/desmat/mapflow/_desmat2".
240412-23:41:23,771 nipype.workflow INFO:
[Node] Cached "_desmat2" - collecting precomputed outputs
240412-23:41:23,772 nipype.workflow INFO:
[Node] "_desmat2" found cached.
240412-23:41:23,774 nipype.workflow INFO:
[Node] Setting-up "_desmat3" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/desmat/mapflow/_desmat3".
240412-23:41:23,776 nipype.workflow INFO:
[Node] Cached "_desmat3" - collecting precomputed outputs
240412-23:41:23,777 nipype.workflow INFO:
[Node] "_desmat3" found cached.
240412-23:41:25,673 nipype.workflow INFO:
[Job 1] Completed (den_workflow.desmat).
240412-23:41:25,677 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:41:27,676 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:41:27,741 nipype.workflow INFO:
[Node] Setting-up "_glm0" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/glm/mapflow/_glm0".
240412-23:41:27,741 nipype.workflow INFO:
[Node] Setting-up "_glm1" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/glm/mapflow/_glm1".
240412-23:41:27,743 nipype.workflow INFO:
[Node] Setting-up "_glm2" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/glm/mapflow/_glm2".
240412-23:41:27,744 nipype.workflow INFO:
[Node] Setting-up "_glm3" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/glm/mapflow/_glm3".
240412-23:41:27,747 nipype.workflow INFO:
[Node] Executing "_glm0" <nipype.interfaces.fsl.model.GLM>
240412-23:41:27,747 nipype.workflow INFO:
[Node] Executing "_glm1" <nipype.interfaces.fsl.model.GLM>
240412-23:41:27,749 nipype.workflow INFO:
[Node] Executing "_glm2" <nipype.interfaces.fsl.model.GLM>
240412-23:41:27,750 nipype.workflow INFO:
[Node] Executing "_glm3" <nipype.interfaces.fsl.model.GLM>
240412-23:41:29,678 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 338.05/338.85, Free processors: 4/8.
Currently running:
* _glm3
* _glm2
* _glm1
* _glm0
240412-23:41:59,159 nipype.workflow INFO:
[Node] Finished "_glm2", elapsed time 31.407655s.
240412-23:41:59,709 nipype.workflow INFO:
[Job 15] Completed (_glm2).
240412-23:41:59,712 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 338.25/338.85, Free processors: 5/8.
Currently running:
* _glm3
* _glm1
* _glm0
240412-23:42:02,40 nipype.workflow INFO:
[Node] Finished "_glm0", elapsed time 34.290153s.
240412-23:42:03,712 nipype.workflow INFO:
[Job 13] Completed (_glm0).
240412-23:42:03,716 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 338.45/338.85, Free processors: 6/8.
Currently running:
* _glm3
* _glm1
240412-23:42:10,682 nipype.workflow INFO:
[Node] Finished "_glm3", elapsed time 42.929641s.
240412-23:42:11,720 nipype.workflow INFO:
[Job 16] Completed (_glm3).
240412-23:42:11,724 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 338.65/338.85, Free processors: 7/8.
Currently running:
* _glm1
240412-23:42:20,113 nipype.workflow INFO:
[Node] Finished "_glm1", elapsed time 52.362164s.
240412-23:42:21,731 nipype.workflow INFO:
[Job 14] Completed (_glm1).
240412-23:42:21,734 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:42:21,817 nipype.workflow INFO:
[Node] Setting-up "_glm0" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/glm/mapflow/_glm0".
240412-23:42:21,822 nipype.workflow INFO:
[Node] Cached "_glm0" - collecting precomputed outputs
240412-23:42:21,823 nipype.workflow INFO:
[Node] "_glm0" found cached.
240412-23:42:21,826 nipype.workflow INFO:
[Node] Setting-up "_glm1" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/glm/mapflow/_glm1".
240412-23:42:21,829 nipype.workflow INFO:
[Node] Cached "_glm1" - collecting precomputed outputs
240412-23:42:21,830 nipype.workflow INFO:
[Node] "_glm1" found cached.
240412-23:42:21,833 nipype.workflow INFO:
[Node] Setting-up "_glm2" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/glm/mapflow/_glm2".
240412-23:42:21,835 nipype.workflow INFO:
[Node] Cached "_glm2" - collecting precomputed outputs
240412-23:42:21,836 nipype.workflow INFO:
[Node] "_glm2" found cached.
240412-23:42:21,839 nipype.workflow INFO:
[Node] Setting-up "_glm3" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/glm/mapflow/_glm3".
240412-23:42:21,841 nipype.workflow INFO:
[Node] Cached "_glm3" - collecting precomputed outputs
240412-23:42:21,842 nipype.workflow INFO:
[Node] "_glm3" found cached.
240412-23:42:23,733 nipype.workflow INFO:
[Job 2] Completed (den_workflow.glm).
240412-23:42:23,737 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:42:25,736 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:42:25,796 nipype.workflow INFO:
[Node] Setting-up "_bpf0" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf0".
240412-23:42:25,798 nipype.workflow INFO:
[Node] Setting-up "_bpf1" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf1".
240412-23:42:25,798 nipype.workflow INFO:
[Node] Setting-up "_bpf2" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf2".
240412-23:42:25,799 nipype.workflow INFO:
[Node] Setting-up "_bpf3" in "/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf3".
240412-23:42:25,803 nipype.workflow INFO:
[Node] Executing "_bpf0" <nipype.interfaces.afni.preprocess.Bandpass>
240412-23:42:25,804 nipype.workflow INFO:
[Node] Executing "_bpf2" <nipype.interfaces.afni.preprocess.Bandpass>
240412-23:42:25,804 nipype.workflow INFO:
[Node] Executing "_bpf1" <nipype.interfaces.afni.preprocess.Bandpass>
240412-23:42:25,804 nipype.workflow INFO:
[Node] Executing "_bpf3" <nipype.interfaces.afni.preprocess.Bandpass>
240412-23:42:25,933 nipype.workflow INFO:
[Node] Finished "_bpf3", elapsed time 0.124582s.
240412-23:42:25,934 nipype.workflow WARNING:
Storing result file without outputs
240412-23:42:25,935 nipype.workflow WARNING:
[Node] Error on "_bpf3" (/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf3)
240412-23:42:25,940 nipype.workflow INFO:
[Node] Finished "_bpf2", elapsed time 0.132846s.
240412-23:42:25,940 nipype.workflow INFO:
[Node] Finished "_bpf1", elapsed time 0.132766s.
240412-23:42:25,941 nipype.workflow WARNING:
Storing result file without outputs
240412-23:42:25,941 nipype.workflow WARNING:
Storing result file without outputs
240412-23:42:25,942 nipype.workflow WARNING:
[Node] Error on "_bpf2" (/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf2)
240412-23:42:25,943 nipype.workflow WARNING:
[Node] Error on "_bpf1" (/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf1)
240412-23:42:25,943 nipype.workflow INFO:
[Node] Finished "_bpf0", elapsed time 0.136747s.
240412-23:42:25,944 nipype.workflow WARNING:
Storing result file without outputs
240412-23:42:25,946 nipype.workflow WARNING:
[Node] Error on "_bpf0" (/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf0)
240412-23:42:27,738 nipype.workflow ERROR:
Node _bpf0 failed to run on host kronos.
240412-23:42:27,740 nipype.workflow ERROR:
Saving crash info to /home/boulakispar/Documents/GitLab/mb_monash/crash-20240412-234227-boulakispar-_bpf0-3ca9a142-ee02-4959-a9af-855aaa3b0d3b.pklz
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/home/boulakispar/miniforge3/envs/mb_monash/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 _bpf0.
Cmdline:
3dBandpass -prefix bpf_filt -dt 1.560000 0.008000 0.090000 /data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf0/glm_residuals.nii
Stdout:
Stderr:
++ 3dBandpass: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: RW Cox
*+ WARNING: (-: For most purposes, 3dTproject is superior to 3dBandpass :-)
*+ WARNING: (-: Even better is to use afni_proc.py for pre-processing!! :-)
** AFNI can't deal with 5 dimensional NIfTI(/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf0/glm_residuals.nii)
** FATAL ERROR: Can't open dataset '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf0/glm_residuals.nii'
** Program compile date = Jul 8 2023
Traceback:
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'out_file' trait of an AFNICommandOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf0/bpf_filt+orig.BRIK' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
outputs = self.aggregate_outputs(runtime)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf0/bpf_filt+orig.BRIK' for output 'out_file' of a Bandpass interface
240412-23:42:27,745 nipype.workflow ERROR:
Node _bpf1 failed to run on host kronos.
240412-23:42:27,747 nipype.workflow ERROR:
Saving crash info to /home/boulakispar/Documents/GitLab/mb_monash/crash-20240412-234227-boulakispar-_bpf1-a3bb1da3-42d7-49b4-9ae8-e06988d2acde.pklz
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/home/boulakispar/miniforge3/envs/mb_monash/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 _bpf1.
Cmdline:
3dBandpass -prefix bpf_filt -dt 1.560000 0.008000 0.090000 /data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf1/glm_residuals.nii
Stdout:
Stderr:
++ 3dBandpass: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: RW Cox
*+ WARNING: (-: For most purposes, 3dTproject is superior to 3dBandpass :-)
*+ WARNING: (-: Even better is to use afni_proc.py for pre-processing!! :-)
** AFNI can't deal with 5 dimensional NIfTI(/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf1/glm_residuals.nii)
** FATAL ERROR: Can't open dataset '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf1/glm_residuals.nii'
** Program compile date = Jul 8 2023
Traceback:
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'out_file' trait of an AFNICommandOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf1/bpf_filt+orig.BRIK' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
outputs = self.aggregate_outputs(runtime)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf1/bpf_filt+orig.BRIK' for output 'out_file' of a Bandpass interface
240412-23:42:27,751 nipype.workflow ERROR:
Node _bpf2 failed to run on host kronos.
240412-23:42:27,752 nipype.workflow ERROR:
Saving crash info to /home/boulakispar/Documents/GitLab/mb_monash/crash-20240412-234227-boulakispar-_bpf2-6bf1f3af-7735-4fe0-a110-41e411055e90.pklz
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/home/boulakispar/miniforge3/envs/mb_monash/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 _bpf2.
Cmdline:
3dBandpass -prefix bpf_filt -dt 1.560000 0.008000 0.090000 /data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf2/glm_residuals.nii
Stdout:
Stderr:
++ 3dBandpass: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: RW Cox
*+ WARNING: (-: For most purposes, 3dTproject is superior to 3dBandpass :-)
*+ WARNING: (-: Even better is to use afni_proc.py for pre-processing!! :-)
** AFNI can't deal with 5 dimensional NIfTI(/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf2/glm_residuals.nii)
** FATAL ERROR: Can't open dataset '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf2/glm_residuals.nii'
** Program compile date = Jul 8 2023
Traceback:
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'out_file' trait of an AFNICommandOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf2/bpf_filt+orig.BRIK' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
outputs = self.aggregate_outputs(runtime)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf2/bpf_filt+orig.BRIK' for output 'out_file' of a Bandpass interface
240412-23:42:27,757 nipype.workflow ERROR:
Node _bpf3 failed to run on host kronos.
240412-23:42:27,758 nipype.workflow ERROR:
Saving crash info to /home/boulakispar/Documents/GitLab/mb_monash/crash-20240412-234227-boulakispar-_bpf3-c04f129a-925a-460f-8f10-6425b1b80c0c.pklz
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/home/boulakispar/miniforge3/envs/mb_monash/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 _bpf3.
Cmdline:
3dBandpass -prefix bpf_filt -dt 1.560000 0.008000 0.090000 /data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf3/glm_residuals.nii
Stdout:
Stderr:
++ 3dBandpass: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: RW Cox
*+ WARNING: (-: For most purposes, 3dTproject is superior to 3dBandpass :-)
*+ WARNING: (-: Even better is to use afni_proc.py for pre-processing!! :-)
** AFNI can't deal with 5 dimensional NIfTI(/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf3/glm_residuals.nii)
** FATAL ERROR: Can't open dataset '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf3/glm_residuals.nii'
** Program compile date = Jul 8 2023
Traceback:
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'out_file' trait of an AFNICommandOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf3/bpf_filt+orig.BRIK' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
outputs = self.aggregate_outputs(runtime)
File "/home/boulakispar/miniforge3/envs/mb_monash/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/data/project/mb_monash/res/preproc/den_workflow/_subject_list_sub-205/bpf/mapflow/_bpf3/bpf_filt+orig.BRIK' for output 'out_file' of a Bandpass interface
240412-23:42:27,763 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 338.85/338.85, Free processors: 8/8.
240412-23:42:29,738 nipype.workflow INFO:
***********************************
240412-23:42:29,739 nipype.workflow ERROR:
could not run node: den_workflow.bpf.a0
240412-23:42:29,741 nipype.workflow INFO:
crashfile: /home/boulakispar/Documents/GitLab/mb_monash/crash-20240412-234227-boulakispar-_bpf0-3ca9a142-ee02-4959-a9af-855aaa3b0d3b.pklz
240412-23:42:29,742 nipype.workflow ERROR:
could not run node: den_workflow.bpf.a0
240412-23:42:29,743 nipype.workflow INFO:
crashfile: /home/boulakispar/Documents/GitLab/mb_monash/crash-20240412-234227-boulakispar-_bpf1-a3bb1da3-42d7-49b4-9ae8-e06988d2acde.pklz
240412-23:42:29,743 nipype.workflow ERROR:
could not run node: den_workflow.bpf.a0
240412-23:42:29,744 nipype.workflow INFO:
crashfile: /home/boulakispar/Documents/GitLab/mb_monash/crash-20240412-234227-boulakispar-_bpf2-6bf1f3af-7735-4fe0-a110-41e411055e90.pklz
240412-23:42:29,745 nipype.workflow ERROR:
could not run node: den_workflow.bpf.a0
240412-23:42:29,746 nipype.workflow INFO:
crashfile: /home/boulakispar/Documents/GitLab/mb_monash/crash-20240412-234227-boulakispar-_bpf3-c04f129a-925a-460f-8f10-6425b1b80c0c.pklz
240412-23:42:29,747 nipype.workflow INFO:
***********************************
It runs correctly until the bandpass step, upon when I get this pathing error that tracks to afni seeing my data as 5d. However, I checked the dimension of my data, and its a standard 4D BOLD img. Can someone tell me where I make the mistake ?
P.S. Sometimes I send messages outside of conventional working hours. Please do not feel pressured to respond outside your own work schedule.
Kind regards,
Boulakis Paradeisios Alexandros, FNRS Aspirant
Physiology of Cognition Lab, GIGA CRC In Vivo Imaging
Allée du 6 Août 8
4000 Liège
Belgium
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