Open tashrifbillah opened 3 years ago
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.
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
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
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
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:
Singularity image
from Dockerhub
:singularity build bidsonym_latest.simg docker://peerherholz/bidsonym
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?
--deid mridefacer
appears to remove given data:mridefacer
block of your nipype pipeline or is the deletion expected upon runtime failure?