MRIQC Not performing segmentation

Hi all,

I am trying to run MRIQC using the bare-metal installation and I am getting the error: AttributeError: ‘_FMRISummaryInputSpec’ object has no attribute ‘seg_file’. The segmentation folder containing segmentation files isn’t produced in the working directory.

My command and output is below:

bash-3.2$ mriqc /Volumes/EXTERNAL/data/ds005 /Volumes/EXTERNAL/data/ds005_QC participant --participant-label 03 --no-sub
201106-13:46:44,67 cli IMPORTANT:

Running MRIQC version 0.15.2+11.g5898396:
  * BIDS dataset path: /Volumes/EXTERNAL/data/ds005.
  * Output folder: /Volumes/EXTERNAL/data/ds005_QC.
  * Analysis levels: ['participant'].

201106-13:56:17,803 nipype.workflow WARNING:
Storing result file without outputs
201106-13:56:17,804 nipype.workflow WARNING:
[Node] Error on “mriqc_wf.funcMRIQC.ReportsWorkflow.BigPlot” (/Users/hannah/work/mriqc_wf/funcMRIQC/ReportsWorkflow/in_file…Volumes…EXTERNAL…data…ds005…sub-03…func…sub-03_task-mixedgamblestask_run-03_bold.nii.gz/BigPlot)
201106-13:56:19,688 nipype.workflow ERROR:
Node BigPlot.a2 failed to run on host Hannah.fios-router.home.
201106-13:56:19,691 nipype.workflow ERROR:
Saving crash info to /Volumes/EXTERNAL/data/ds005_QC/logs/crash-20201106-135619-hannah-BigPlot.a2-adc17f06-f853-4c97-b486-3bb4737ba1d3.txt
Traceback (most recent call last):
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 419, in run
runtime = self._run_interface(runtime)
File “/usr/local/lib/python3.8/site-packages/niworkflows/interfaces/plotting.py”, line 65, in _run_interface
seg_file=self.inputs.in_segm if isdefined(self.inputs.seg_file) else None,
AttributeError: ‘_FMRISummaryInputSpec’ object has no attribute ‘seg_file’

Traceback (most recent call last):
File “/usr/local/bin/mriqc”, line 8, in
sys.exit(main())
File “/usr/local/lib/python3.8/site-packages/mriqc/cli/run.py”, line 69, in main
mriqc_wf.run(**config.nipype.get_plugin())
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py”, line 632, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py”, line 164, in run
self._clean_queue(jobid, graph, result=result)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py”, line 227, in _clean_queue
raise RuntimeError("".join(result[“traceback”]))
RuntimeError: Traceback (most recent call last):
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 419, in run
runtime = self._run_interface(runtime)
File “/usr/local/lib/python3.8/site-packages/niworkflows/interfaces/plotting.py”, line 65, in _run_interface
seg_file=self.inputs.in_segm if isdefined(self.inputs.seg_file) else None,
AttributeError: ‘_FMRISummaryInputSpec’ object has no attribute ‘seg_file’

If I use the -m flag (e.g. < mriqc /Volumes/EXTERNAL/data/ds005 /Volumes/EXTERNAL/data/ds005_QC participant --participant-label 03 --no-sub -m T1w > ), then the anatomical workflow will run successfully and the segmentation folder and all files is produced, but whenever I try to run mriqc with functional files, I get the ‘seg_file’ error.

It seems like whenever there are functional files, mriqc is skipping segmentation and then failing. I am very new to mriqc and am not as familiar with nipype workflows. Can somebody point in a direction to de-bug this?

I am, unfortunately, not able to use Docker/Singularity due to security restrictions at my institution.

Thanks,
Hannah

Attached is my error log:

Node: mriqc_wf.funcMRIQC.ReportsWorkflow.BigPlot
Working directory: /Users/hannah/work/mriqc_wf/funcMRIQC/ReportsWorkflow/in_file…Volumes…EXTERNAL…data…ds005…sub-03…func…sub-03_task-mixedgamblestask_run-03_bold.nii.gz/BigPlot

Node inputs:

dvars =
fd =
fd_thres = 0.2
in_func =
in_mask =
in_segm =
in_spikes_bg =
outliers =
tr = None

Traceback (most recent call last):
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/usr/local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 419, in run
runtime = self._run_interface(runtime)
File “/usr/local/lib/python3.8/site-packages/niworkflows/interfaces/plotting.py”, line 65, in _run_interface
seg_file=self.inputs.in_segm if isdefined(self.inputs.seg_file) else None,
AttributeError: ‘_FMRISummaryInputSpec’ object has no attribute ‘seg_file’