Log files not found for QSIPrep

Software Support
1

Hello,

After running QSIPrep, the log files are nowhere to be found.
The output directory is correctly specified, and there are no partial logs in the temporary directory either.
Has anyone encountered a similar issue?

I appreciate your help in advance.

2

Hi @kifli1 and welcome to neurostars!

For future posts, please use the Software Support category for these kind of issues, which prompts you for important information.

It would help to know your QSIPrep command, what version you used, whether the job ran successfully, and what exists in the output directory (e.g., with the tree command).

Best,
Steven

3

Dear Steven,

Thank you for your prompt response.

QSIPrep command:

[‘singularity’, ‘run’, ‘–cleanenv’, ‘-B’, ‘/data/pipeline/sandbox_data/’, ‘–bind’, ‘/usr/local/freesurfer/7.3.2/license.txt:/license.txt’, ‘/data/pipeline/sandbox_data//resources/qsiprep-0.21.3.sif’,
‘/data/pipeline/sandbox_data/bids/’,
‘/data/pipeline/sandbox_data/bids/derivatives’, ‘participant’,
‘–participant-label’, ‘02’,
‘–output-resolution’, ‘1.5’,
‘–skip-bids-validation’,
‘–pepolar-method’, ‘DRBUDDI’,
‘–freesurfer-input’, ‘/data/pipeline/sandbox_data/bids/derivatives/fmriprep/sourcedata/freesurfer/02’,
‘–fs-license-file’, ‘/license.txt’,
‘–nthreads’, ‘12’,
‘–mem_mb’, ‘95000’,
‘-w’, ‘/data/pipeline/sandbox_data/tmp/qsiprep_workflow_02/work’]

Version: 0.19.0

Yes, it ran successfully.

Content of output directory:

├── dataset_description.json
├── dwiqc.json
├── logs
│ ├── CITATION.html
│ ├── CITATION.md
│ └── CITATION.tex
├── sub-01
│ ├── anat
│ ├── figures
│ ├── ses-01
│ └── ses-02
├── sub-01.html
├── sub-02
│ ├── anat
│ ├── figures
│ ├── ses-01
│ └── ses-02
├── sub-02.html
├── sub-03
│ ├── anat
│ ├── figures
│ └── ses-01
└── sub-03.html

Thank you again for your help.

4

The logging print outs that you see during the run are not saved to a text file - it’s up to you to redirect them to a file or not. The critical processing-related info is all in the html file. The command you posted also won’t print much to the terminal during the run. I typically add two verbose flags when I run qsiprep (ie -v -v)