Error on "gen_eddy_files"

[h-w-k]

• dmriprep version: 0.5.0rc0
• Operating System: Linux

Description

I ran dmriprep on Phillips data using the following dMRIPREP command,

dmriprep /work /output participant --participant_label sub-002 --fs-license-file /main/licens.txt --output-spaces T1w --use-syn-sdc --skip-bids-validation -w /main/WORK

Errors occured in "gen_eddy_files" shown in html report
"Node Name: dmriprep_wf.single_subkect_002_wf.dwi_preproc_ses_01_run001_wf.eddy.wf.gen_eddy_files
Node Name: dmriprep_wf.single_subkect_002_wf.dwi_preproc_ses_01_run001_dti_wf.eddy_wf.gen_eddy_files"

Please kindly advise how to fix it.

I think it is about PhaseEncodingDirection and Total Readout Time, which are required in the node. If it is the case, how could I input the required data in dMRIPREP command line?

Thank you very much.

[margokersey]

Hi, I believe I am also having the same issue as you. In the output file on my HPC I am getting the error:
nipype.workflow ERROR: Node gen_eddy_files failed to run on host (hostname here)

I tried adding more memory to the job file (20G) but it did not change the result. I believe I have the B0FieldIdentifier and B0FieldSource fields filled out correctly in the JSON files. I also have the IntendedFor field filled out just in case.

in AP phase encoding JSON:
"TotalReadoutTime": 0.0305196,
"PhaseEncodingDirection": "j-",
"IntendedFor": ["ses-20220822/dwi/sub-34115_ses-20220822_acq-b500_dir-30_dwi.nii.gz",
"ses-20220822/dwi/sub-34115_ses-20220822_acq-b1000_dir-64_dwi.nii.gz",
"ses-20220822/dwi/sub-34115_ses-20220822_acq-b2500_dir-96_dwi.nii.gz"],
"B0FieldIdentifier": "pepolar"

in PA phase encoding JSON:
"TotalReadoutTime": 0.0305196,
"PhaseEncodingDirection": "j",
"IntendedFor": ["ses-20220822/dwi/sub-34115_ses-20220822_acq-b500_dir-30_dwi.nii.gz",
"ses-20220822/dwi/sub-34115_ses-20220822_acq-b1000_dir-64_dwi.nii.gz",
"ses-20220822/dwi/sub-34115_ses-20220822_acq-b2500_dir-96_dwi.nii.gz"],
"B0FieldIdentifier": "pepolar"

in b500/b1000/b2500 JSON:
"TotalReadoutTime": 0.0305196,
"PhaseEncodingDirection": "j-",
"B0FieldSource": "pepolar"

In the subject's html file, the errors are the following:

(Removed in_meta field for privacy)

Errors

Node Name: dmriprep_wf.single_subject_01_wf.dwi_preproc_ses_20220822_acq_b2500_dir_96_wf.eddy_wf.gen_eddy_files

File: /out/dmriprep/sub-01/log/20230306-131934_90711f6c-910e-4008-a322-2bdfba99d6a5/crash-20230306-132033-mkersey-gen_eddy_files-e43cd7c6-3ff5-4576-bd0f-913add0d63e7.txt
Working Directory: /out/workdir/dmriprep_wf/single_subject_01_wf/dwi_preproc_ses_20220822_acq_b2500_dir_96_wf/eddy_wf/gen_eddy_files
Inputs:

• function_str: def gen_eddy_textfiles(in_file, in_meta): """ Generate the acquisition-parameters and index files for FSL eddy_openmp. Examples -------- >>> out_acqparams, out_index = gen_eddy_textfiles( ... "dwi.nii.gz", ... {"PhaseEncodingDirection": "j-", "TotalReadoutTime": 0.005}, ... ) >>> Path(out_acqparams).read_text() '0 -1 0 0.0050000' >>> Path(out_index).read_text() '1 1 1 1 1 1' """ from pathlib import Path import nibabel as nb from sdcflows.utils.epimanip import get_trt from nipype.utils.filemanip import fname_presuffix # Generate output file name out_acqparams = fname_presuffix( in_file, suffix="_acqparams.txt", use_ext=False, ) pe_dir = in_meta["PhaseEncodingDirection"] fsl_pe = ["0"] * 3 fsl_pe["ijk".index(pe_dir[0])] = "-1" if pe_dir.endswith("-") else "1" # Write to the acqp file try: Path(out_acqparams).write_text( f"{' '.join(fsl_pe)} {get_trt(in_meta, in_file=in_file):0.7f}" ) except ValueError: Path(out_acqparams).write_text(f"{' '.join(fsl_pe)} {0.05}") out_index = fname_presuffix( in_file, suffix="_index.txt", use_ext=False, ) Path(out_index).write_text(f"{' '.join(['1'] * nb.load(in_file).shape[3])}") return out_acqparams, out_index

Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 434, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
File "", line 37, in gen_eddy_textfiles
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1208, in write_text
with self.open(mode='w', encoding=encoding, errors=errors) as f:
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1176, in open
opener=self._opener)
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1030, in _opener
return self._accessor.open(self, flags, mode)
OSError: [Errno 30] Read-only file system: '/data/sub-01/ses-20220822/dwi/sub-01_ses-20220822_acq-b2500_dir-96_dwi_acqparams.txt'

Node Name: dmriprep_wf.single_subject_01_wf.dwi_preproc_ses_20220822_acq_b1000_dir_64_wf.eddy_wf.gen_eddy_files

File: /out/dmriprep/sub-01/log/20230306-131934_90711f6c-910e-4008-a322-2bdfba99d6a5/crash-20230306-132033-mkersey-gen_eddy_files-f50f3e90-2439-4367-9e40-d609448c1ea0.txt
Working Directory: /out/workdir/dmriprep_wf/single_subject_01_wf/dwi_preproc_ses_20220822_acq_b1000_dir_64_wf/eddy_wf/gen_eddy_files
Inputs:

• function_str: def gen_eddy_textfiles(in_file, in_meta): """ Generate the acquisition-parameters and index files for FSL eddy_openmp. Examples -------- >>> out_acqparams, out_index = gen_eddy_textfiles( ... "dwi.nii.gz", ... {"PhaseEncodingDirection": "j-", "TotalReadoutTime": 0.005}, ... ) >>> Path(out_acqparams).read_text() '0 -1 0 0.0050000' >>> Path(out_index).read_text() '1 1 1 1 1 1' """ from pathlib import Path import nibabel as nb from sdcflows.utils.epimanip import get_trt from nipype.utils.filemanip import fname_presuffix # Generate output file name out_acqparams = fname_presuffix( in_file, suffix="_acqparams.txt", use_ext=False, ) pe_dir = in_meta["PhaseEncodingDirection"] fsl_pe = ["0"] * 3 fsl_pe["ijk".index(pe_dir[0])] = "-1" if pe_dir.endswith("-") else "1" # Write to the acqp file try: Path(out_acqparams).write_text( f"{' '.join(fsl_pe)} {get_trt(in_meta, in_file=in_file):0.7f}" ) except ValueError: Path(out_acqparams).write_text(f"{' '.join(fsl_pe)} {0.05}") out_index = fname_presuffix( in_file, suffix="_index.txt", use_ext=False, ) Path(out_index).write_text(f"{' '.join(['1'] * nb.load(in_file).shape[3])}") return out_acqparams, out_index

Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 434, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
File "", line 37, in gen_eddy_textfiles
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1208, in write_text
with self.open(mode='w', encoding=encoding, errors=errors) as f:
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1176, in open
opener=self._opener)
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1030, in _opener
return self._accessor.open(self, flags, mode)
OSError: [Errno 30] Read-only file system: '/data/sub-01/ses-20220822/dwi/sub-01_ses-20220822_acq-b1000_dir-64_dwi_acqparams.txt'

Node Name: dmriprep_wf.single_subject_01_wf.fmap_preproc_wf.wf_pepolar_fmap0.concat_blips

File: /out/dmriprep/sub-01/log/20230306-131934_90711f6c-910e-4008-a322-2bdfba99d6a5/crash-20230306-132035-mkersey-concat_blips-90c5cd72-c066-4afe-95f1-3446cca0a283.txt
Working Directory: /out/workdir/dmriprep_wf/single_subject_01_wf/fmap_preproc_wf/wf_pepolar_fmap0/concat_blips
Inputs:

• allow_4D: True
• in_files:
  Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
  result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
  result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
  return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
  result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 434, in run
  runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/nibabel.py", line 171, in _run_interface
  img_4d = nb.concat_images(nii_list)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/funcs.py", line 141, in concat_images
  raise ValueError(f'Affine for image {i} does not match affine for first image')
  ValueError: Affine for image 1 does not match affine for first image

Node Name: dmriprep_wf.single_subject_01_wf.dwi_preproc_ses_20220822_acq_b500_dir_30_wf.eddy_wf.gen_eddy_files

File: /out/dmriprep/sub-01/log/20230306-131934_90711f6c-910e-4008-a322-2bdfba99d6a5/crash-20230306-132035-mkersey-gen_eddy_files-82dfde7a-9c8a-4a6c-ab0b-d1ffd0a3c6d6.txt
Working Directory: /out/workdir/dmriprep_wf/single_subject_01_wf/dwi_preproc_ses_20220822_acq_b500_dir_30_wf/eddy_wf/gen_eddy_files
Inputs:

• function_str: def gen_eddy_textfiles(in_file, in_meta): """ Generate the acquisition-parameters and index files for FSL eddy_openmp. Examples -------- >>> out_acqparams, out_index = gen_eddy_textfiles( ... "dwi.nii.gz", ... {"PhaseEncodingDirection": "j-", "TotalReadoutTime": 0.005}, ... ) >>> Path(out_acqparams).read_text() '0 -1 0 0.0050000' >>> Path(out_index).read_text() '1 1 1 1 1 1' """ from pathlib import Path import nibabel as nb from sdcflows.utils.epimanip import get_trt from nipype.utils.filemanip import fname_presuffix # Generate output file name out_acqparams = fname_presuffix( in_file, suffix="_acqparams.txt", use_ext=False, ) pe_dir = in_meta["PhaseEncodingDirection"] fsl_pe = ["0"] * 3 fsl_pe["ijk".index(pe_dir[0])] = "-1" if pe_dir.endswith("-") else "1" # Write to the acqp file try: Path(out_acqparams).write_text( f"{' '.join(fsl_pe)} {get_trt(in_meta, in_file=in_file):0.7f}" ) except ValueError: Path(out_acqparams).write_text(f"{' '.join(fsl_pe)} {0.05}") out_index = fname_presuffix( in_file, suffix="_index.txt", use_ext=False, ) Path(out_index).write_text(f"{' '.join(['1'] * nb.load(in_file).shape[3])}") return out_acqparams, out_index

Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 434, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
File "", line 37, in gen_eddy_textfiles
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1208, in write_text
with self.open(mode='w', encoding=encoding, errors=errors) as f:
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1176, in open
opener=self._opener)
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1030, in _opener
return self._accessor.open(self, flags, mode)
OSError: [Errno 30] Read-only file system: '/data/sub-01/ses-20220822/dwi/sub-01_ses-20220822_acq-b500_dir-30_dwi_acqparams.txt'

Thank you so much in advance for any insight on how to fix this problem!!