Hello! I’m fairly new to fmriprep and feel like I’m missing something relatively obvious, but I can’t seem to find a solution anywhere so I’m hoping someone on here can help me.
- when I try to run fmriprep on my data it fails BIDS validation due to the file names but I’m not sure why these aren’t in bids format (this is attempting to run for 1 subject with 3 separate tasks):
You are using fMRIPrep-20.2.5, and a newer version of fMRIPrep is available: 21.0.2.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
bids-validator@1.4.0
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 compatible. 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 https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (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-003/ses-1/func/task-affvis/sub-003_ses-1_task-affvis_bold.nii
Evidence: sub-003_ses-1_task-affvis_bold.nii
./sub-003/ses-1/func/task-affvis/sub-003_ses-1_task-affvis_events.tsv
Evidence: sub-003_ses-1_task-affvis_events.tsv
./sub-003/ses-1/func/task-facegender/sub-003_ses-1_task-facegender_bold.nii
Evidence: sub-003_ses-1_task-facegender_bold.nii
./sub-003/ses-1/func/task-facegender/sub-003_ses-1_task-facegender_events.tsv
Evidence: sub-003_ses-1_task-facegender_events.tsv
./sub-003/ses-1/func/task-facememory/sub-003_ses-1_task-facememory_bold.nii
Evidence: sub-003_ses-1_task-facememory_bold.nii
./sub-003/ses-2/func/task-affvis/sub-003_ses-2_task-affvis_bold.nii
Evidence: sub-003_ses-2_task-affvis_bold.nii
./sub-003/ses-2/func/task-affvis/sub-003_ses-2_task-affvis_events.tsv
Evidence: sub-003_ses-2_task-affvis_events.tsv
./sub-003/ses-2/func/task-facegender/sub-003_ses-2_task-facegender_bold.nii
Evidence: sub-003_ses-2_task-facegender_bold.nii
./sub-003/ses-2/func/task-facegender/sub-003_ses-2_task-facegender_events.tsv
Evidence: sub-003_ses-2_task-facegender_events.tsv
./sub-003/ses-2/func/task-facememory/sub-003_ses-2_task-facememory_bold.nii
Evidence: sub-003_ses-2_task-facememory_bold.nii
- If I skip bids validation and run fmriprep, there seems to be an issue with the slice timing correction. I get the following output:
220520-16:27:14,113 nipype.workflow INFO:
No single-band-reference found for sub-003_ses-1_task-affvis_bold.nii.
220520-16:27:14,373 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 1.71s.
220520-16:27:14,410 nipype.interface INFO:
We advise you to upgrade DIPY version. This upgrade will open access to more function
220520-16:27:14,411 nipype.interface INFO:
We advise you to upgrade DIPY version. This upgrade will open access to more function
220520-16:27:14,412 nipype.interface INFO:
We advise you to upgrade DIPY version. This upgrade will open access to more models
220520-16:27:14,513 nipype.workflow INFO:
No single-band-reference found for sub-003_ses-1_task-facegender_bold.nii.
220520-16:27:14,645 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 1.71s.
220520-16:27:14,738 nipype.workflow INFO:
No single-band-reference found for sub-003_ses-1_task-facememory_bold.nii.
220520-16:27:14,867 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 1.71s.
220520-16:27:14,970 nipype.workflow INFO:
No single-band-reference found for sub-003_ses-2_task-affvis_bold.nii.
220520-16:27:15,101 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 1.71s.
220520-16:27:15,197 nipype.workflow INFO:
No single-band-reference found for sub-003_ses-2_task-facegender_bold.nii.
220520-16:27:15,409 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 1.71s.
220520-16:27:15,504 nipype.workflow INFO:
No single-band-reference found for sub-003_ses-2_task-facememory_bold.nii.
This seems to occur for all tasks and I’m not sure why the slice timing correction doesn’t work. The relevant parts of my json files are as follows, though let me know if it’d be useful to have the whole json file:
{ "RepetitionTime": 3.5,
"SliceTiming":[0.0000,
0.0875,
0.1750,
0.2625,
0.3500,
0.4375,
0.5250,
0.6125,
0.7000,
0.7875,
0.8750,
0.9625,
1.0500,
1.1375,
1.2250,
1.3125,
1.4000,
1.4875,
1.5750,
1.6625,
1.7500,
1.8375,
1.9250,
2.0125,
2.1000,
2.1875,
2.2750,
2.3625,
2.4500,
2.5375,
2.6250,
2.7125,
2.8000,
2.8875,
2.9750,
3.0625,
3.1500,
3.2375,
3.3250,
3.4125]
}