I’m a newbie for DWI data analyses and also qsiprep.
I’m working on DWI preprocessing with qsiprep and have encountered an issue. I have dwi data, anatomy image in BIDS format, but it seems like that dwi data is not recognized by qsiprep somehow.
I got an error message as below when the folder contained anat and dwi folders under the subject folder. The folders are like this s016/dwi, s016/anat , but dwi preprocessing doesn’t work. It worked when I tried --anat-only.
Command used (and if a helper script was used, a link to the helper script or the command generated):
Script I used : ubuntu@qsi:/mnt$ singularity run --cleanenv -B /mnt qsiprep-0.19.0.sif /mnt/data /mnt/derivatives participant --participant_label sub-s016 --output-resolution 1.0 --fs-license-file /home/ubuntu/license.txt --skip-bids-validation
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
Error message :
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py", line 950, in build_qsiprep_workflow
retval['workflow'] = init_qsiprep_wf(
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/base.py", line 228, in init_qsiprep_wf
single_subject_wf = init_single_subject_wf(
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/base.py", line 497, in init_single_subject_wf
raise Exception("No dwi images found for participant {}. "
Exception: No dwi images found for participant s016. All workflows require dwi images unless --anat-only is specified.
Screenshots / relevant information:
Could you help me out for this? I have checked bidsignore, there’s nothing special…
For future reference, the Software Support post category comes with a post template, please use this is future posts. I have added it back for you and reorganized your post.
I expect the answer will become obvious if you do not --skip-bids-validation. Can you return the report of the BIDS validator, and also the output from tree /mnt? Please make sure to format the terminal outputs like this using the </> button in the text editor or surroudning the text in tick marks (these things: ```)
Also, in general it is good to specifiy a working directory with the -w flag.
Thank you very much for the answer! I’ll follow the template next time.
Without --skip-bids-validation,
I got this message.
For more information, check the migration guide at Migrating your code to SDK for JavaScript V3 - AWS SDK for JavaScript
1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatibl e. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a “.bidsignore” file in your dataset (see GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure for details). Please note that der ived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
./sub-s016/dwi/sub-s016_dir-AP-dwi.bval
Evidence: sub-s016_dir-AP-dwi.bval
./sub-s016/dwi/sub-s016_dir-AP-dwi.bvec
Evidence: sub-s016_dir-AP-dwi.bvec
./sub-s016/dwi/sub-s016_dir-AP-dwi.json
Evidence: sub-s016_dir-AP-dwi.json
./sub-s016/dwi/sub-s016_dir-AP-dwi.nii.gz
Evidence: sub-s016_dir-AP-dwi.nii.gz
./sub-s016/dwi/sub-s016_dir-PA-dwi.bval
Evidence: sub-s016_dir-PA-dwi.bval
./sub-s016/dwi/sub-s016_dir-PA-dwi.bvec
Evidence: sub-s016_dir-PA-dwi.bvec
./sub-s016/dwi/sub-s016_dir-PA-dwi.json
Evidence: sub-s016_dir-PA-dwi.json
./sub-s016/dwi/sub-s016_dir-PA-dwi.nii.gz
Evidence: sub-s016_dir-PA-dwi.nii.gz
When I tried tree /mnt, I got nothing due to an error. It worked /home, but doesn’t work subfolders of mnt.
. [error opening dir]
0 directories, 0 files
The folder structure is like this : /mnt/data/subjfolder/dwi/sub-s016_dir-PA-dwi.nii.gz
@jsein is right, but I’ll just add that it is easier for us to read the output when your format it as code using the </> button in the text editor, so it looks like this:
## For more information, check the migration guide at [Migrating your code to SDK for JavaScript V3 - AWS SDK for JavaScript](https://a.co/7PzMCcy)
1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatibl e. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a “.bidsignore” file in your dataset (see [GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure](https://github.com/bids-standard/bids-validator#bidsignore) for details). Please note that der ived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
./sub-s016/dwi/sub-s016_dir-AP-dwi.bval
Evidence: sub-s016_dir-AP-dwi.bval
./sub-s016/dwi/sub-s016_dir-AP-dwi.bvec
Evidence: sub-s016_dir-AP-dwi.bvec
./sub-s016/dwi/sub-s016_dir-AP-dwi.json
Evidence: sub-s016_dir-AP-dwi.json
./sub-s016/dwi/sub-s016_dir-AP-dwi.nii.gz
Evidence: sub-s016_dir-AP-dwi.nii.gz
./sub-s016/dwi/sub-s016_dir-PA-dwi.bval
Evidence: sub-s016_dir-PA-dwi.bval
./sub-s016/dwi/sub-s016_dir-PA-dwi.bvec
Evidence: sub-s016_dir-PA-dwi.bvec
./sub-s016/dwi/sub-s016_dir-PA-dwi.json
Evidence: sub-s016_dir-PA-dwi.json
./sub-s016/dwi/sub-s016_dir-PA-dwi.nii.gz
Evidence: sub-s016_dir-PA-dwi.nii.gz