Closed yyang1234 closed 3 weeks ago
I am not 100% sure as to what is going on here but I suspect that that it may be related to the pybids database.
Do you get the same errors if you run the commands with the --reset_database
flag
bidsmreye /Volumes/ssd/fmriprep /Volumes/ssd/mreyeputput/localizer participant --action all --task wordLocalizer --reset_database
Will try to improve the error message and the FAQ to give better hints
unfortunately, it didn't solve the problem. New error messages are as below. It seems that bidsmreye are able to index all the three tasks ['aliceLocalizer', 'numMVPA', 'wordLocalizer'], but it can't process task 'aliceLocalizer' and 'wordLocalizer ' Do you have any idea about it?
RuntimeError: Input dataset /Volumes/ssd/fmriprep does not have any data to process
for filter
{'datatype': 'func', 'desc': 'preproc', 'suffix': '^bold$', 'extension': 'nii.*',
'task': ['wordLocalizer'], 'space': ['MNI152NLin2009cAsym', 'T1w'], 'run': [1, 2, 3,
4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]}.
This dataset contains subjects: ['02', '03', '04', '05', '06', '07', '08', '09',
'10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22',
'23'].This dataset contains tasks: ['aliceLocalizer', 'numMVPA', 'wordLocalizer'].Is
your dataset a BIDS derivative dataset?
Check the FAQ for more information:
https://bidsmreye.readthedocs.io/en/latest/FAQ.html
damn...
is the dataset on GIN by any chance?
will make it easier for me to test things
not yet I have been putting off pushing my data to GIN... But now I have a good reason to do it. I'll let you know when it's done.
maybe start by pushing a couple of subjects only: should be enough for me to start testing
Hi, here's the data https://gin.g-node.org/ying1234/fmriprep_demo let me know if you have a problem accessing it.
looks I can access the data will start downloading so I can test
Great! There's no rush so take your time.
I can reproduce the issue!!! 🎉
and I think I spotted the issue
should be fixed by #212
I could run it on the 3 tasks or just the word localizer
will cut a new release soon so you can install from pypi or from docker hub
I want to run bidsmreye on fmriprep-preprocessed data. In the fmriprep-preprocessed data folder, I have three task:
task-wordLocalizer
task-numMVPA
task-aliceLocalizer
.When I run
bidsmreye /Volumes/ssd/fmriprep /Volumes/ssd/mreyeputput/localizer participant
, I only got results fromtask-numMVPA
. If I specific the task to be processed bybidsmreye /Volumes/ssd/fmriprep /Volumes/ssd/mreyeputput/localizer participant --task wordLocalizer
, I got an errorRuntimeError: Input dataset /Volumes/ssd/fmriprep does not have any data to process for filter {this_filter}
I put the full error message and the structure of bids_dir below