AKA Jak oszukałem mriqc, żeby wziął atlas tpl-MNI152NLin2009cAsym/cohort-2

UWAGA - TO NIC NIE ZMIENIA to znaczy zmiana templatu na bardzij odpowiedni nie ma znacznego wpływu na parametry (sprawdzone na tylko kilku przykładach). Prawdopodobnie chodzi o to, że mriqc używa innego brain extraction niż fmriprep (SynthStrip vs ANTS).

datalad install -r ///templateflow
cd templateflow
datalad get -r tpl-MNIPediatricAsym/cohort-2

This command can be executed from within mriqc container eg. singularity shell /cvmfs/neurodesk.ardc.edu.au/containers/mriqc_24.0.2_20241108/mriqc_24.0.2_20241108.simg

Then You need to modify module load wrapper:

copy "original wrapper" ~/mriqc-wrapper

#!/usr/bin/env bash
export PWD=`pwd -P`
singularity --silent exec --cleanenv --env DISPLAY=$DISPLAY  $neurodesk_singularity_opts --pwd "$PWD" --bind /home/jovyan/config.py:/opt/conda/lib/python3.11/site-packages/mriqc/config.py --bind /home/jovyan/templateflow:/templateflow/ /cvmfs/neurodesk.ardc.edu.au/containers/mriqc_24.0.2_20241108/mriqc_24.0.2_20241108.simg mriqc "$@"

in config.py:
....
template_id: str = 'MNIPediatricAsymCohort2'
....

Above will enable modification of config.py and loading templateflow from mounted directory.

Then You need to prepare legacy tpl-MNI152NLin2009cAsym from MNI152NLin2009cAsym/cohort-2/, because get_template() does not take cohort as an argument:

cp -L templateflow2/templateflow/tpl-MNIPediatricAsym/cohort-2/* templateflow/tpl-MNIPediatricAsymCohort2/
-L because it is a git-annex repository and uses symbolic links

rename.ul _cohort-2 Cohort2 *.nii.gz
to get git of unsupported label

Future plan: Look up into fmriprep code to get an idea how they resolve such a template id tpl-MNI152NLin2009cAsym:cohort-2