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psychoinformatics-de / datalad-hirni

DataLad extension for (semi-)automated, reproducible processing of (medical/neuro)imaging data
http://datalad.org
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FR: automatically call mridefacer when running spec2bids using --anonymize #144

Open pvavra opened 4 years ago

pvavra commented 4 years ago

currenlty, the mridefacer procedure doesn't work for me at all. This is how a call looks like to me (after I manually git annex get .the singularity container)

datalad run-procedure hirni-mridefacer sub-001/ses-001/anat/sub-001_ses-001_T1w.nii.gz                                                                   
[INFO   ] Running procedure hirni-mridefacer

and that's it.

Inspecting the code, shows that the function isn't getting enough love :) (e.g. no help, i.e. not all args being processes).

In addition, it should be automatically called when using the --anonymize flag when converting to bids. My current understanding is that heudiconv is run in a /tmp-... folder; mridefacer should be applied there, before the images are moved into their final destination.

@bpoldrack If you want me to post the issues which directly speak to the hirni-toolbox code there, let me know. Given that this should be part of the datalad-hirni interface, I thought here might be a more intuitive place for people to be looking for this kind issue.

bpoldrack commented 4 years ago

If you want me to post the issues which directly speak to the hirni-toolbox code there, let me know. Given that this should be part of the datalad-hirni interface, I thought here might be a more intuitive place for people to be looking for this kind issue.

Agree. Right place in that case.

Re actual issue: Never seen that happening. This might need your help to reproduce.

pvavra commented 4 years ago

might be an issue of me using datalad 0.12rc4?

What would help reproducing this? Giving you access to a shared medusa folder and the python environment?