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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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[BUG] No error raised if no subjects found in the input directory #348

Closed shuo-zhou closed 7 years ago

shuo-zhou commented 7 years ago

The terminal shows "/usr/local/miniconda/lib/python3.5/site-packages/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed warnings.warn('cmp not installed')" when I using fmriprep in the docker container. I think cmp is optional for nipype, is this package requested in fmriprep. I trid to install the cmp package (https://github.com/LTS5/cmp), but the outcome is the same. By the way, nipype is not installed at "/usr/local/miniconda/lib/python3.5/site-packages/" on my computer. Is there any mistake I made in running fmriprep?

effigies commented 7 years ago

So that's a warning, not an error. I wouldn't worry about it, as FMRIPREP doesn't use those features of nipype.

Apart from this warning, are things running as expected?

shuo-zhou commented 7 years ago

Only create two empty folders (derivatives and log) in the out folder

chrisgorgo commented 7 years ago

Did it report any errors? Could you post the full log?

On Sat, Jan 28, 2017 at 2:28 PM, sz144 notifications@github.com wrote:

Only create two empty folders (derivatives and log) in the out folder

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shuo-zhou commented 7 years ago

It seems run well when given the pramater of participant_label But according to the instruction on https://github.com/BIDS-Apps/fmriprep, when I removed the argument --participant_label for getting all subjects processed, only two empty folders derivatives and log created in the out folder. the full log is attached 2

chrisgorgo commented 7 years ago

Thanks for reporting. We'll investigate.

shuo-zhou commented 7 years ago

I just found the datasets I applied now (the initial relaese of openfmri project) are not in the format of BIDs. I tried to process the revision dataset I used previously without the --participant_label argument and it runs well. But no errors or warnings other than cmp warning report when processing all subjects of the datasets in other format.

chrisgorgo commented 7 years ago

This has been recently fixed in MRIQC, but I think we still need to add it to FMRIPREP.

effigies commented 7 years ago

Closed in #558.