Upgrade BIDScoin to v4.3.0 (#594)

* - Upgrade BIDScoin to 4.3.0
- Remove tools that need FSL or FreeSurfer

* Fix URL typo

* Fix versionstring replacement

recipes/bidscoin/README.md

@@ -1,27 +1,23 @@
 
 ----------------------------------
-## bidscoin/4.2.1 ##
-Contains a collection of tools needed for DICOM to BIDS conversion, as well as MRS spectroscopy and physiological data to BIDS conversion
+## bidscoin/4.3.0 ##
+Contains a GUI and CLI tools needed for DICOM to BIDS conversion, as well as MRS spectroscopy and physiological data to BIDS conversion
 
-Tools included:
+Tools included (NB: some tools that depend on FSL or FreeSurfer are not included):
 ```
-bidscoin: https://bidscoin.readthedocs.io/en/4.2.1
+dcm2niix: https://github.com/rordenlab/dcm2niix (v1.0.20240202)
+spec2nii: https://github.com/wtclarke/spec2nii (v0.7.2)
+bidscoin: https://bidscoin.readthedocs.io/en/4.3.0
     bidscoin
     bidscoiner
     bidseditor
     bidsmapper
     bidsparticipants
-    deface
     dicomsort
     echocombine
-    medeface
     physio2tsv
     plotphysio
     rawmapper
-    skullstrip
-    slicereport
-dcm2niix: v1.0.20230411 https://github.com/rordenlab/dcm2niix
-spec2nii: v0.7.0: https://github.com/wtclarke/spec2nii
 ```
 
 Example converting dicom to BIDS: 
@@ -35,14 +31,13 @@ bidscoiner inputfolder bidsoutputfolder
 ```
 
 More documentation can be found here:
-https://bidscoin.readthedocs.io/en/4.2.1
-
+https://bidscoin.readthedocs.io/
 
 Citation:
 ```
 Zwiers MP, Moia S, Oostenveld R. BIDScoin: A User-Friendly Application to Convert Source Data to Brain Imaging Data Structure. Front Neuroinform. 2022 Jan 13;15:770608. doi: 10.3389/fninf.2021.770608. PMID: 35095452; PMCID: PMC8792932.
 ```
 
-To run container outside of this environment: `ml bidscoin/4.2.1`
+To run container outside of this environment: ml bidscoin/4.3.0
 
 ----------------------------------

recipes/bidscoin/build.sh

@@ -3,30 +3,27 @@ set -e
 
 # this template file builds tools required for dicom conversion to bids
 export toolName='bidscoin'
-export toolVersion='4.2.1'
-# Don't forget to update version change in README.md!!!!!
+export toolVersion='4.3.0'    # Don't forget to update version change in README.md!!!!!
 
 if [ "$1" != "" ]; then
     echo "Entering Debug mode"
+    export BIDSCOIN_DEBUG=TRUE
     export debug=$1
 fi
 
 source ../main_setup.sh
 
-# Changes made to .def file:
-# 1. turned the apt-get install to neurodocker install
-# 2. put commands with cd with && in between
-# TODO: update these list items to better reflect the changes made
-neurodocker generate ${neurodocker_buildMode} `# Based on Singularity .def file provided by bidscoin at https://github.com/Donders-Institute/bidscoin/blob/master/singularity.def` \
-    `# Install the latest dcm2niix from source` \
+# Changes made to .def file: turned the apt-get install to neurodocker install and use Ubuntu/Qt6
+neurodocker generate ${neurodocker_buildMode} `# Based on Singularity .def file provided by bidscoin at https://github.com/Donders-Institute/bidscoin/blob/master/apptainer.def` \
     --pkg-manager apt \
     --base-image debian:stable \
     --env DEBIAN_FRONTEND=noninteractive \
     --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
     --run="chmod +x /usr/bin/ll" \
     --run="mkdir -p ${mountPointList}" \
+    `# Install the latest dcm2niix from source` \
     --install git build-essential cmake \
-    --run "export GIT_SSL_NO_VERIFY=1 && git clone https://github.com/rordenlab/dcm2niix.git" `# first command solves some issue with the close as explaine here: https://stackoverflow.com/questions/21181231/server-certificate-verification-failed-cafile-etc-ssl-certs-ca-certificates-c` \
+    --run "export GIT_SSL_NO_VERIFY=1 && git clone https://github.com/rordenlab/dcm2niix.git" `# first command solves some issue with the clone, see: https://stackoverflow.com/questions/21181231/server-certificate-verification-failed-cafile-etc-ssl-certs-ca-certificates-c` \
     --run "cd dcm2niix; mkdir build && cd build; cmake ..; make install" \
     `#  Install curl (sometimes needed by dcm2niix)` \
     --install curl \
@@ -36,11 +33,16 @@ neurodocker generate ${neurodocker_buildMode} `# Based on Singularity .def file
     `# NOTE: PyQt5 is installed as Debian package to solve dependencies issues occurring when installed with pip.` \
     --install python3-pyqt5 \
     --miniconda version=latest \
-		pip_install='bidscoin[spec2nii2bids,deface]@git+https://github.com/Donders-Institute/bidscoin@v4.2.1+qt5' \
-   --env DEPLOY_BINS=bidscoin:bidscoiner:bidseditor:bidsmapper:bidsparticipants:deface:dicomsort:echocombine:medeface:physio2tsv:plotphysio:rawmapper:skullstrip:slicereport:dcm2niix:pydeface:spec2nii \
+		pip_install="bidscoin[spec2nii2bids]@git+https://github.com/Donders-Institute/bidscoin@v${toolVersion}+qt5" \
+   --env DEPLOY_BINS=bidscoin:bidscoiner:bidseditor:bidsmapper:bidsparticipants:dicomsort:echocombine:physio2tsv:plotphysio:rawmapper:dcm2niix:spec2nii \
    --copy README.md /README.md \
   > ${toolName}_${toolVersion}.Dockerfile
 
 if [ "$1" != "" ]; then
    ./../main_build.sh
 fi
+
+# Test image with:
+# sudo docker run --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix bidscoin_${toolVersion}:TAG bidscoin -t
+# sudo docker run -it -v /root:/root --entrypoint /bin/bash -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix bidscoin_${toolVersion}:TAG
+# bidscoin -t

recipes/bidscoin/test.sh

@@ -1,3 +1,4 @@
  export QT_DEBUG_PLUGINS=1
  bidscoin -t
- bidseditor myproject/bids
+ bidseditor myproject/bids
+ # sudo docker run --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix  bidscoin_4.3.0:20240219 bidscoin -t