I attached a screenshot from the error we are receiving. We are at a loss and do not know what is going wrong… We put the structure into an online bids validator and everything seems to be fine and according to BIDS structure. However, when wanting to run fmriprep it does not work… Anybody having experiences with the first error and tips how to work around it?
It looks like the actual bids dataset is in /BIDS/5007. Also, any files/directory you want the bids validation to ignore (such as dcm2bids temp files) can go in a .bidsignore in the main bids folder.
When using --skip_bids_validation, I actually do get something different now and it seems that it is working? However, in the designated output map I do not see any output… I will apply the tips that you suggested!
This is the folder with the data: dbstore/Rijnstate/SYNAPSE/BIDS/sub-007/ses-01/ (in right BIDS format), so ’ BIDS’ would be the root map that I bound to the singularity container. However, when running BIDS validator, I also get the error that fmriprep is validating other maps that are not in BIDS, but one map higher (SYNAPSE). I do not quite understand why it is doing that… but I will put all unnecessary data in another map (.bidsignore).
Other possibility to what Steven said: put your code (either related to BIDS conversion or to the code your used to run the experiment) in a code folder rather than in a script folder.
You most likely don’t want to do that because you are then mixing raw and derivatives data (and will very likely make the validator complain).
Using something like /BIDS/derivatives for the output should be sufficient.
This was indeed the case, I changed it to BIDS/derivatives. And fmriprep was finally running for 4 hours, which is good. However, what I do not understand is that it put the derivatives folder in the map that is one level higher than the BIDS map, even though the BIDS map is my root map… The structure is like this ~/SYNAPSE/BIDS/[raw data structure], and fmriprep made a new folder derivatives in /SYNAPSE/derivatives. Any idea why? My commmand for the output was /BIDS/derivatives, so I assumed that it would make a new folder in folder BIDS.
I assume that we need to get some sort of preprocessed file out of fmriprep, but we only got the logs… Without any warning or error messages in this path:
In your singularity container, you mounted the folder SYNAPSE AS BIDS. So within the singularity container BIDS will point to your local folder SYNAPSE.
In regards to only seeing the logs, are the jobs still running? Outputs are copied over at the end of the process (intermediary files are made in the work directory).
fMRIPrep can take a long time to run, depending on your computational resources, number of scans per subject, and processing options. I would give it a day, and if you still see nothing or if there’s a crash, then we can debug further.