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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
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MPRAGE-based T1w sequence - Return code: 1 #1006

Closed y-x-y-x closed 1 year ago

y-x-y-x commented 2 years ago

Hello,

I am working on MRIQC on a Ubuntu 18.04 desktop. I have tried to implement it in both Docker and Singularity containers for one particular subject in BIDS format. The image that I am working on is of MPRAGE-based T1w sequence. However, both failed and returned the same error. Meanwhile the same code works with other dataset of T1w sequences.

I attach the error logs below:

220714-10:14:42,751 nipype.workflow WARNING: Storing result file without outputs 220714-10:14:42,751 nipype.workflow WARNING: [Node] Error on "mriqc_wf.anatMRIQC.synthstrip_wf.synthstrip" (/home/tehyx/work/mriqc_wf/anatMRIQC/synthstrip_wf/_infile..data..sub-001..anat..sub-001_T1w.nii.gz/synthstrip) 220714-10:14:43,186 nipype.workflow ERROR: Node synthstrip.a0 failed to run on host administrator-System-Product-Name. 220714-10:14:43,198 nipype.workflow ERROR: Saving crash info to /out/logs/crash-20220714-101443-tehyx-synthstrip.a0-85f1f797-d97c-4be2-9218-cc3a7a28fb17.txt Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 60, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface self.raise_exception(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 741, in raise_exception raise RuntimeError( RuntimeError: Command: synthstrip -b 1 -i /home/tehyx/work/mriqc_wf/anatMRIQC/synthstrip_wf/_infile..data..sub-001..anat..sub-001_T1w.nii.gz/pre_n4/clipped_corrected.nii.gz --model /opt/freesurfer/models/synthstrip.1.pt -o clipped_corrected_desc-brain.nii.gz -m clipped_corrected_desc-brain_mask.nii.gz Standard output: Configuring model on the CPU Using custom model weights Input image read from: /home/tehyx/work/mriqc_wf/anatMRIQC/synthstrip_wf/_infile..data..sub-001..anat..sub-001_T1w.nii.gz/pre_n4/clipped_corrected.nii.gz Standard error: Traceback (most recent call last): File "/opt/conda/bin/synthstrip", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/mriqc/synthstrip/cli.py", line 137, in main sdt_target = resample_like( File "/opt/conda/lib/python3.8/site-packages/mriqc/synthstrip/cli.py", line 231, in resample_like return Affine(reference=target).apply(image, output_dtype=output_dtype, cval=cval) File "/opt/conda/lib/python3.8/site-packages/nitransforms/base.py", line 282, in apply _as_homogeneous(self.map(_ref.ndcoords.T), dim=_ref.ndim) File "/opt/conda/lib/python3.8/site-packages/nitransforms/linear.py", line 174, in map return affine.dot(coords).T[..., :-1] numpy.core._exceptions.MemoryError: Unable to allocate 3.38 GiB for an array with shape (4, 113246208) and data type float64 Return code: 1

Traceback (most recent call last): File "/opt/conda/bin/mriqc", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/mriqc/cli/run.py", line 158, in main mriqc_wf.run(**_plugin) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 632, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 184, in run self._clean_queue(jobid, graph, result=result) File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 256, in _clean_queue raise RuntimeError("".join(result["traceback"])) RuntimeError: Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 60, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface self.raise_exception(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 741, in raise_exception raise RuntimeError( RuntimeError: Command: synthstrip -b 1 -i /home/tehyx/work/mriqc_wf/anatMRIQC/synthstrip_wf/_infile..data..sub-001..anat..sub-001_T1w.nii.gz/pre_n4/clipped_corrected.nii.gz --model /opt/freesurfer/models/synthstrip.1.pt -o clipped_corrected_desc-brain.nii.gz -m clipped_corrected_desc-brain_mask.nii.gz Standard output: Configuring model on the CPU Using custom model weights Input image read from: /home/tehyx/work/mriqc_wf/anatMRIQC/synthstrip_wf/_infile..data..sub-001..anat..sub-001_T1w.nii.gz/pre_n4/clipped_corrected.nii.gz Standard error: Traceback (most recent call last): File "/opt/conda/bin/synthstrip", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/mriqc/synthstrip/cli.py", line 137, in main sdt_target = resample_like( File "/opt/conda/lib/python3.8/site-packages/mriqc/synthstrip/cli.py", line 231, in resample_like return Affine(reference=target).apply(image, output_dtype=output_dtype, cval=cval) File "/opt/conda/lib/python3.8/site-packages/nitransforms/base.py", line 282, in apply _as_homogeneous(self.map(_ref.ndcoords.T), dim=_ref.ndim) File "/opt/conda/lib/python3.8/site-packages/nitransforms/linear.py", line 174, in map return affine.dot(coords).T[..., :-1] numpy.core._exceptions.MemoryError: Unable to allocate 3.38 GiB for an array with shape (4, 113246208) and data type float64 Return code: 1

May I know what could be the problem and how should I resolve it? Thanks.

Best Regards, Yu Xuan

oesteban commented 1 year ago

Looks like you are exceeding memory limits:

numpy.core._exceptions.MemoryError: Unable to allocate 3.38 GiB for an array with shape (4, 113246208) and data type float64