Hi Stefan,

I have a small suggestion re lines 1376- in KUL_dcm2bids.sh, the code block creating the .bidsignore file.
This is handy, except for the fact that in case you want to add study-specific lines to your .bidsignore file (as I had done prior to running KUL_dcm2bids.sh on my first subject), they seem to disappear after running the script because the .bidsignore file gets overwritten, and this happens again after running every subject.

If I understand things correctly, this can easily be changed by replacing > with >> on line 1383, as this would append the new lines to any existing .bidsignore file rather than overwrite the existing file? I tested this locally (without adding nor committing) and it works, but the problem then is that it appends the same lines to .bidsignore after running the script for each subject, which does not harm, but is not very clean? Hence, another option may be to check whether .bidsignore already exists and then decide based on that whether to append or newly create? Not sure whether or how line 1379 does that? It does not seem to do it in my hands.

Or maybe you see a different option?

I wanted to check by you before branching and submitting a pull request, but happy to do so if you like?!

Other than this small issue, the script works great - really helpful!

Best wishes,

Lukas

When running dcm2bids conversion I get following message

jblomm6$ KUL_dcm2bids.sh -d DICOM/ -o OUTPUT/ -c STUDY_CONFIG/study_config.txt -p 01 Darwin Your mrtrix3 RC3 subversion is 20 You need mrtrix3 RC3 subversion => 133

However, I just updated my mrtrix:

jblomm6$ mrconvert -version == mrconvert 3.0_RC3_latest-20-gc13c7052 == 64 bit release version, built Oct 25 2019, using Eigen 3.3.5 Author(s): J-Donald Tournier ([email protected]) and Robert E. Smith ([email protected]) Copyright (c) 2008-2018 the MRtrix3 contributors.

On a more general note, would it be possible to just give a warning if versions are not up to date or an argument to check version checking? This might be handy if people work with certain dev packages or so.

Any chance there's a Docker/Singularity image for the software suite? I have a use case for the T1w/FLAIR ratio in my data.

Thanks

Hi I see some local path in KUL_T1T2FLAIRMTR_ratio.sh code at line , how should be solved?
777:

Method 3 - Cappelle & Sunaert

                echo "  performing second (Cappelle) nonlinear histogram matching"

                M3_template_T1w=/home/stefan/DATA2/Sarah/REVIEW/Cappelle2021_final/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_T1w.nii.gz
                M3_template_T2w=/home/stefan/DATA2/Sarah/REVIEW/Cappelle2021_final/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_T2w.nii.gz
                M3_template_FLAIR=/home/stefan/DATA2/Sarah/REVIEW/Cappelle2021_final/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_FLAIR.nii.gz

                M3_template_mask_4_T1w=/home/stefan/DATA2/Sarah/REVIEW/Cappelle2021_final/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_mask_4_T1w.nii.gz
                M3_template_mask_4_T2w_and_FLAIR=/home/stefan/DATA2/Sarah/REVIEW/Cappelle2021_final/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_mask_4_T2w_and_FLAIR.nii.gz

Hi Stefan,

in KUL_main_functions it should be noted that a newer version of mrtrix is out
lines 402-405 should be replaced with:
elif [ $mrtrix_version_revision_major -eq 3 ]; then
mrtrix3new=1
kul_echo "you are using a new version of MRTrix3 $mrtrix_version_revision_major $mrtrix_version_revision_minor but not the latest"
elif [ $mrtrix_version_revision_major -eq 4 ]; then

However, I would suggest to also allow for newer version than you know in future use, as well as older that still might work, but just give a warning that the code is not tested for this