Open shawnrhoads opened 9 months ago
Hi shawnrhoads, I've run into the same problem as yours. Have you found a way to work around it?
Hi shawnrhoads, I've run into the same problem as yours. Have you found a way to work around it?
Yes, I believe it is because the app is no longer compatible with the older BIDS format where fmriprep outputs to BIDSroot/derivatives/fmriprep
. Instead, the fmriprep output should be located in BIDSroot/derivatives
. See here for explanation.
However, I chose not to restructure my data since many of my scripts rely on the older BIDS structure (maybe I will try on a different dataset in the future). It would be helpful if you can confirm that this resolves your issue though for future!
What version of the bids app were you using?
v4.0.3
Describe your problem in detail.
Hello!
I am testing out the new PyMVPA BIDS-App on one of my datasets (I am excited about the promise of this new tool)! However, I am unable get past the
participant_prep
stage. I was directed to submit an issue here.I created a singularity image using this command:
Then, I tried running
participant_prep
for one subject using the following command:This creates
/SR/subjects/derivatives/pymvpa
and/SR/subjects/derivatives/pymvpa/masks
, but the data for that subject is not prepped (no output folder named "sub-501").I get the following warnings (this is everything that is written to the terminal):
I suspect it is somehow not looping through
sub_IDs
at lines 168-186 inrun.py
. Could it also be related at all to theLC_ALL
locale warning?I can confirm that my directory is BIDS compliant. I added the
--skip_bids_validator
flag because it appears thatbids-validator
is not installed in the container? This is the additional warning I get when I run the command above without skipping validation.What command did you run?
(Update) Also tried this command:
Describe what you expected.
I expected the command to create a new directory at
/bids_dataset/derivatives/pymvpa/sub-501
with runs concatenated.