Data formatted according to a validatable standard? Please provide the output of the validator:
Attention: I converted my data from Nifiti to Dicom, but it was validated by Bidscoin.
Relevant log outputs (up to 20 lines):
Error:
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/opt/conda/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/workflow.py", line 115, in build_workflow
retval["workflow"] = init_fmriprep_wf()
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py", line 91, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py", line 413, in init_single_subject_wf
func_preproc_wf = init_func_preproc_wf(bold_file, has_fieldmap=has_fieldmap)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/bold/base.py", line 204, in init_func_preproc_wf
nvols = nb.load(bold_file[0] if isinstance(bold_file, (list, tuple)) else bold_file).shape[3]
IndexError: tuple index out of range
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues
C:\Users\Carlos Leandro\Desktop\dados>python -m fmriprep_docker "/Users/Carlos Leandro/Desktop/dados/bids" "/Users/Carlos Leandro/dados/derivatives" participant --participant-label 01 --skip-bids-validation --md-only-boilerplate --fs-license-file "/Users/Carlos Leandro/Desktop/sourcedata/license.txt" --output-spaces MNI152NLin2009cAsym:res-2 --stop-on-first-crash -w "/Users/Carlos Leandro/Desktop/dados/workdir" --mem-mb 6000
Warning: <8GB of RAM is available within your Docker environment.
Some parts of fMRIPrep may fail to complete.
Continue anyway? [y/N]y
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.17 -it -v C:\Users\Carlos Leandro\Desktop\sourcedata\license.txt:/opt/freesurfer/license.txt:ro -v C:\Users\Carlos Leandro\Desktop\dados\bids:/data:ro -v C:\Users\Carlos Leandro\dados\derivatives:/out -v C:\Users\Carlos Leandro\Desktop\dados\workdir:/scratch nipreps/fmriprep:22.1.1 /data /out participant --participant-label 01 --skip-bids-validation --md-only-boilerplate --stop-on-first-crash --mem-mb 6000 -w /scratch --output-spaces MNI152NLin2009cAsym:res-2
--topup-max-vols input is no longer used and the flag will be removed in a future release.
230203-17:16:47,802 nipype.workflow IMPORTANT:
Running fMRIPrep version 22.1.1
License NOTICE ##################################################
fMRIPrep 22.1.1
Copyright 2022 The NiPreps Developers.
This product includes software developed by
the NiPreps Community (https://nipreps.org/).
Portions of this software were developed at the Department of
Psychology at Stanford University, Stanford, CA, US.
This software redistributes the versioneer Python package, which is
Public domain source code.
This software is also distributed as a Docker container image.
The bootstraping file for the image ("Dockerfile") is licensed
under the MIT License.
This software may be distributed through an add-on package called
"Docker Wrapper" that is under the BSD 3-clause License.
#################################################################
230203-17:16:47,858 nipype.workflow IMPORTANT:
Building fMRIPrep's workflow:
* BIDS dataset path: /data.
* Participant list: ['01'].
* Run identifier: ***********
* Output spaces: MNI152NLin2009cAsym:res-2.
* Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/opt/conda/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/workflow.py", line 115, in build_workflow
retval["workflow"] = init_fmriprep_wf()
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py", line 91, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py", line 413, in init_single_subject_wf
func_preproc_wf = init_func_preproc_wf(bold_file, has_fieldmap=has_fieldmap)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/bold/base.py", line 204, in init_func_preproc_wf
nvols = nb.load(bold_file[0] if isinstance(bold_file, (list, tuple)) else bold_file).shape[3]
IndexError: tuple index out of range
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues
C:\Users\Carlos Leandro\Desktop\dados>python -m fmriprep_docker "/Users/Carlos Leandro/Desktop/dados/bids" "/Users/Carlos Leandro/dados/derivatives" participant --participant-label 01 --md-only-boilerplate --fs-license-file "/Users/Carlos Leandro/Desktop/sourcedata/license.txt" --output-spaces MNI152NLin2009cAsym:res-2 --stop-on-first-crash -w "/Users/Carlos Leandro/Desktop/dados/workdir" --mem-mb 6000
Warning: <8GB of RAM is available within your Docker environment.
Some parts of fMRIPrep may fail to complete.
Continue anyway? [y/N]y
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.17 -it -v C:\Users\Carlos Leandro\Desktop\sourcedata\license.txt:/opt/freesurfer/license.txt:ro -v C:\Users\Carlos Leandro\Desktop\dados\bids:/data:ro -v C:\Users\Carlos Leandro\dados\derivatives:/out -v C:\Users\Carlos Leandro\Desktop\dados\workdir:/scratch nipreps/fmriprep:22.1.1 /data /out participant --participant-label 01 --md-only-boilerplate --stop-on-first-crash --mem-mb 6000 -w /scratch --output-spaces MNI152NLin2009cAsym:res-2
--topup-max-vols input is no longer used and the flag will be removed in a future release.
bids-validator@1.8.0
1: [ERR] Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR)
./sub-01/func/sub-01_task-fMRITESTE6_run-1_echo-1_bold.json
Evidence: .TaskName should be string
Please visit https://neurostars.org/search?q=JSON_SCHEMA_VALIDATION_ERROR for existing conversations about this issue.
2: [ERR] Bold scans must be 4 dimensional. (code: 54 - BOLD_NOT_4D)
./sub-01/func/sub-01_task-fMRITESTE6_run-1_echo-1_bold.nii.gz
Evidence: header field "dim" = 3,112,112,1
Please visit https://neurostars.org/search?q=BOLD_NOT_4D for existing conversations about this issue.
3: [ERR] "SliceTiming" value/s contains invalid value as it is greater than RepetitionTime. SliceTiming values should be in seconds not milliseconds (common mistake). (code: 66 - SLICETIMING_VALUES_GREATOR_THAN_REPETITION_TIME)
./sub-01/func/sub-01_task-fMRITESTE6_run-1_echo-1_bold.nii.gz
Evidence: 5.083
Please visit https://neurostars.org/search?q=SLICETIMING_VALUES_GREATOR_THAN_REPETITION_TIME for existing conversations about this issue.
4: [ERR] NIfTI file's header is missing time dimension information. (code: 75 - NIFTI_PIXDIM4)
./sub-01/func/sub-01_task-fMRITESTE6_run-1_echo-1_bold.nii.gz
Please visit https://neurostars.org/search?q=NIFTI_PIXDIM4 for existing conversations about this issue.
1: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)
Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
9 Files, 38.93KB MRI
1 - Subject
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
Traceback (most recent call last):
File "/opt/conda/bin/fmriprep", line 8, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/run.py", line 42, in main
parse_args()
File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/parser.py", line 810, in parse_args
validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/utils/bids.py", line 186, in validate_input_dir
subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])
File "/opt/conda/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', '/data', '-c', '/tmp/tmpsmpu096o.json']' returned non-zero exit status 1.
Yes, your data are not BIDS valid, according to the official BIDS validator. Looking at the errors 1-by-1:
All you need to do here is add TaskName: "fMRITESTE6" to the BOLD json file
I have no idea why a BOLD file would only have one volume, and also it’s strange that you only have 3 slices in the X direction. You might want to reconfirm that you converted Nifti from DCM correctly.
Both of these errors would probably be fixed by confirming you are using the most recent version of dcm2niix.
In short, I would suggest using a tool such as dcm2bids to go from dicoms to a BIDS valid dataset. There are tutorials on the website I linked. If done properly, it should take care of all the errors.
