Open bcmcpher opened 1 week ago
That's strange, because it ran without issue on my Linux test VM. Maybe there has been an update of some dependency, causing this issue, I will have a look
I did what you described to reproduce the issue, but my test ran normally:
$ apptainer exec bidscoin.sif bidscoin -t
INFO | --------- Testing the BIDScoin's core functionality ---------
INFO | Running bidsmap checks:
INFO | Reading: /home/marzwi/.bidscoin/4.4.0/templates/bidsmap_dccn.yaml
INFO | Checking the bidsmap run-items:
VERBOSE | Could not validate every run-item in the bidsmap
VERBOSE | Checking the template bidsmap datatypes:
SUCCESS | All datatypes and options in the template bidsmap are valid
INFO | Testing the PyQt GUI setup:
qt.qpa.theme.dbus: Session DBus not running.
qt.qpa.theme.dbus: Application will not react to setting changes.
Check your DBus installation.
SUCCESS | The GUI seems to work OK
INFO | Testing the DRMAA setup:
WARNING | The DRMAA library could not be imported. This is OK if you want to run pydeface locally and not use the option to distribute jobs on a compute cluster
Could not find drmaa library. Please specify its full path using the environment variable DRMAA_LIBRARY_PATH
INFO | Executable BIDScoin tools:
INFO | - bidscoin
INFO | - bidscoiner
INFO | - bidseditor
INFO | - bidsmapper
INFO | - bidsparticipants
INFO | - deface
INFO | - dicomsort
INFO | - echocombine
INFO | - fixmeta
INFO | - medeface
INFO | - physio2tsv
INFO | - plotphysio
INFO | - rawmapper
INFO | - skullstrip
INFO | - slicereport
INFO | Installed template bidsmaps (/home/marzwi/.bidscoin/4.4.0/templates):
INFO | - bidsmap_bids2bids
INFO | - bidsmap_dccn (default)
INFO | - bidsmap_sst
INFO | Installed plugins (/home/marzwi/.bidscoin/4.4.0/plugins):
INFO | - dcm2niix2bids
INFO | - nibabel2bids
INFO | - spec2nii2bids
INFO | --------- Testing the 'dcm2niix2bids' plugin ---------
INFO | Testing the dcm2niix2bids installation:
VERBOSE | Command:
dcm2niix -v
VERBOSE | Output:
Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC12.2.0 x86-64 (64-bit Linux)
v1.0.20240202
SUCCESS | The 'dcm2niix2bids' plugin functioned correctly
INFO | --------- Testing the 'nibabel2bids' plugin ---------
INFO | Testing the nibabel2bids installation:
INFO | Nibabel version: 5.2.1
SUCCESS | The 'nibabel2bids' plugin functioned correctly
INFO | --------- Testing the 'spec2nii2bids' plugin ---------
INFO | Testing the spec2nii2bids installation:
VERBOSE | Command:
spec2nii -v
VERBOSE | Output:
0.8.4
SUCCESS | The 'spec2nii2bids' plugin functioned correctly
SUCCESS | All tests finished successfully :-)
I followed the instructions here for using
bidsmapper
from a singularity container. However, I receive the following error:To reproduce: Follow the tutorial instructions on the website in a clean environment.
Expected behavior:
bidsmapper
GUI should openSoftware version
Potential Fix: If I set
export QT_DEBUG_PLUGINS=1
, I get a verbose log, with the only obvious error being:I was unable to bind
libqgtk3.so
into that location from my host, but if I did a--sandbox
build of the container, I was able to runapt install libqgtk-3-0
, which added some dependencies. With those additional libraries I was able to launch thebidsmapper
GUI.I believe adding
libqgtk-3-0
to the build instructions as part of theconda
environment or w/apt
will fix this issue.