Hi,
I am using dwiresponse dhollander and it is working fine in Docker but not in Singularity/apptainer because it tries to write in a read-only system.
I created a /etc/mrtrix.conf and the container sees it:
Apptainer> cat /etc/mrtrix.conf
ScriptScratchDir:/flywheel/v0/output/tmp
TmpFileDir:/flywheel/v0/output/tmp
When using with -debug, it can read the files.
[...]
maskfilter -quiet -force -npass 1 OR_roi3_R_subj.nii.gz dilate - | mrthreshold -force -abs 0.5 - OR_roi3_R_subj_dil-1.nii.gz
mrthreshold: e[00;31m[WARNING] existing output files will be overwritten
mrthreshold: e[00;32m[INFO] reading config file "/etc/mrtrix.conf"...e[0m
mrthreshold: e[00;34m[DEBUG] reading key/value file "/etc/mrtrix.conf"...e[0m
mrthreshold: e[00;34m[DEBUG] No config file found at "/export/home/glerma/.mrtrix.conf"e[0m
mrthreshold: e[00;32m[INFO] opening image
[...]
But dwi2response dhollander is not reading it it seems, and it is failing everytime saying that it cannot write in a non-write folder.
[...]
dwi2response: e[01;31m[ERROR] Unhandled Python exception:e[0m
dwi2response: e[01;31m[ERROR]e[0m e[03;32mOSError: [Errno 30] Read-only file system: [...]
[...]
I am using mrtrix 3.0.4
What can I do to fix this? I haven’t checked if it is only this function the one acting out, I can test others if it is helpful.
thanks!
Gari