CORR_cat12.8.1/code/doCSV+QC_ses.sh

#/bin/bash
#
# create CVS for atlases included in CAT peprocessing and get QC
#
### use 'true' as input var if dataset containes sites: "./doCSV+QC_ses.sh true"

sites=$1

mkdir outputs
DS=$(basename $PWD)

### if there are sites, things get complicated ###
if ( ${sites} ); then
    datalad get */sub*/ses*/report/cat_*.xml */sub*/ses*/label/cat*.xml
  for site in *; do
    if [ -d ${site} ] && [ ${site} != "logs" ] && [ ${site} != "code" ] \
        && [ ${site} != "inputs" ] && [ ${site} != "outputs" ]; then
        echo ${site}
        cd ${site}
        echo "table name: ${DS2}"
        for sub in sub-*; do
            for subses in $sub/ses-*; do
                echo "./../code/xml2csv_ses.py ../outputs/${site} ${subses}"
                ./../code/xml2csv_ses.py ../outputs/${site} ${subses}
            done
        done
        cd ..
    fi
  done
else
  datalad get sub*/ses*/report/cat_*.xml sub*/ses*/label/cat*.xml
  for sub in sub-*; do
      for subses in $sub/ses-*; do
        ./code/pipeline/xml2csv/xml2csv_ses.py outputs/${DS} ${subses}
      done
  done
fi