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Donders-Institute / bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS
https://bidscoin.readthedocs.io
GNU General Public License v3.0
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PAR / REC to BIDS #173

Closed marcelzwiers closed 1 year ago

marcelzwiers commented 1 year ago

Discussed in https://github.com/Donders-Institute/bidscoin/discussions/167

Originally posted by **Freeklinders** January 31, 2023 Dear Marcel, I managed to bidscoin all the files in my dataset, though I keep receiving the following errors for all my files when trying to validate the new bids folder; ERROR CODE 1: (NOT INCLUDED): Files with such naming scheme are not part of BIDS specification. ERROR CODE 2: ACQ_NAME_CONTAIN_ILLEGAL_CHARACTER acq Name contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spe structure. My (bids) folder structure is as follows (example field map): BIDS_con_new/sub-1001/fmap/sub-1001_acq-WIPB0epiSENSE_magnitude_fieldmaphz.json In the bids mapper all my files were green and I received the same error when I left out the whole acquisition field in the bids mapper (thereby getting rid of the capitals). Do you have any idea what I am doing wrong? Thanks a lot in advance! Best, Freek
marcelzwiers commented 1 year ago

I think I have an idea what is causing this, namely that dcm2niix produced a nifti-file without an accompanying json sidecar file? Can you confirm this @Freeklinders?

Freeklinders commented 1 year ago

Hi Marcel,

All images have an accompanying .json file!

marcelzwiers commented 1 year ago

Mhhh, strange. And did you get any BIDScoin warnings or errors? (you can still see them in the logfile in yourbidsfolder/code/bidscoin)

Freeklinders commented 1 year ago

2023-02-14 11:15:43 - bidscoin - ERROR Failed to run: module add dcm2niix;dcm2niix -b y -z y -i n -f "sub-1077_acq-sT1W3DTFE32channel_T1w" -o "/data/fjlinders/Data_TMS_BIDS/BIDS_con_new/sub-1077/anat" "/data/fjlinders/Data_TMS_BIDS/RAW/sub-1077/1077_1_sT1W_3D_TFE_32_channel_2_1.PAR" Errorcode 0: /bin/sh: module: command not found

This one I get for every participant!

marcelzwiers commented 1 year ago

That error is innocent (and will no longer appear in the latest version of the code). I'm puzzled, perhaps you can upgrade to the latest version and run the bidsmapper/bidscoiner like this:

pip install --force-reinstall --no-deps git+https://github.com/Donders-Institute/bidscoin
SET BIDSCOIN_DEBUG=TRUE

And then run your bidsmapper / bidscoiner. Would be a big help if you can send me the resulting bidscoiner.log file

marcelzwiers commented 1 year ago

I would like to solve your issue, but I need more information to do so. By any chance, can you share a sample of your fieldmap data with me?

marcelzwiers commented 1 year ago

I am closing this due to a lack of information, feel free to re-open it.