1234567891011121314151617181920212223242526272829303132333435363738 |
- #/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
|