mridefacer removes given data

[tashrifbillah]

--deid mridefacer appears to remove given data:

• Firstly, mridefacer doesn't run because of this. I affected your change, still it does not run.
• After every runtime failure, I can't find my given data anymore. It's just deleted. Anything wrong in the mridefacer block of your nipype pipeline or is the deletion expected upon runtime failure?

[PeerHerholz]

Ahoi hoi @tashrifbillah,

thanks for reporting, I completely missed this.
I just updated several mridefacer parts of BIDSonym to fix this issue. It was indeed an error/problem within the function/workflow. I built and tested the container locally and everything seemed to work fine. Once the build on docker hub finished, you could download the updated version, i.e. latest, and try again. If you don't mind, please let us know if things also worked on your end.

[tashrifbillah]

Hello again, are we sure that you have uploaded the updated version? I did:

singularity pull docker://peerherholz/bidsonym

And the new image still run into the same issue with given data removal and mridefacer unbound variable:

Singularity> /mridefacer/mridefacer --apply /data/pnl/U01_HCP_Psychosis/data_processing/BIDS/rawdata.mridefacer/sourcedata/bidsonym/sub-2004/sub-2004_ses-1_T1w.nii.gz --outdir /data/pnl/U01_HCP_Psychosis/data_processing/BIDS/rawdata.mridefacer/sub-2004/ses-1/anat

/mridefacer/mridefacer: line 275: dim4: unbound variable

[PeerHerholz]

Ahoi hoi,

hm, strange. I'm certain that the version I tested and which worked is up on Dockerhub.

Could you provide more information on how you're utilizing BIDSonym and the dataset you're running it on?
Is this how you call it?

Singularity> /mridefacer/mridefacer --apply /data/pnl/U01_HCP_Psychosis/data_processing/BIDS/rawdata.mridefacer/sourcedata/bidsonym/sub-2004/sub-2004_ses-1_T1w.nii.gz --outdir /data/pnl/U01_HCP_Psychosis/data_processing/BIDS/rawdata.mridefacer/sub-2004/ses-1/anat

[tashrifbillah]

Is this how you call it?

That's the step failed under:

bidsonym pwd participant --brainextraction bet --bet_frac 0.5 --skip_bids_validation --deid mridefacer --deface_t2w --participant_label 001

[PeerHerholz]

Ahoi hoi @tashrifbillah,

sorry for the late reply. I tested things further and there are no problems on my end, neither with the Singularity image nor mridefacer. I'm running Singularity 3.5.1 within Ubuntu 18.04 via Vagrant on macOS. Here are the steps I did:

• get the Singularity image from Dockerhub:

singularity build bidsonym_latest.simg docker://peerherholz/bidsonym

• run it on a test dataset/participant:

singularity run --cleanenv -B /vagrant/bidsonym_test/:/bids_dir bidsonym_latest.simg /bids_dir participant \
--participant_label 01 --deid mridefacer --del_meta "InstitutionAddress" --brainextraction bet --bet_frac 0.5 \
--skip_bids_validation --deface_t2w

As you can see, I used the --cleanenv flag and mounted the BIDS root directory. Maybe this, the Singularity version and build process is something to check in your setup?