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@@ -14,16 +14,20 @@
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# DEFINE ALL PATHS:
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# ==============================================================================
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PATH_BASE="${HOME}"
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+# path to the project root directory
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+PATH_ROOT="${PATH_BASE}/highspeed"
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# define the name of the project:
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-PROJECT_NAME="highspeed"
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+PROJECT_NAME="highspeed-bids"
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+# define the path to the project folder:
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+PATH_PROJECT="${PATH_ROOT}/${PROJECT_NAME}"
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# define the path to the input directory:
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-PATH_INPUT="${PATH_BASE}/${PROJECT_NAME}/rawdata/mri"
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+PATH_INPUT="${PATH_PROJECT}/mri"
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# define the path to the output directory
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-PATH_OUTPUT="${PATH_BASE}/${PROJECT_NAME}/bids"
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+PATH_OUTPUT="${PATH_PROJECT}"
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# define the path to the singularity container:
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-PATH_CONTAINER="${PATH_BASE}/tools/heudiconv/heudiconv_0.6.0.sif"
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+PATH_CONTAINER="${PATH_PROJECT}/tools/heudiconv/heudiconv_0.6.0.sif"
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# define the path to the code main directory:
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-PATH_CODE="${PATH_BASE}/${PROJECT_NAME}/${PROJECT_NAME}_analysis/code"
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+PATH_CODE="${PATH_PROJECT}/code"
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# path to the heudiconv heuristic file:
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HEURISTIC_FILE="highspeed_heudiconv_heuristic.py"
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# define path to the python executable file that anonymizes the subject ids:
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@@ -31,17 +35,12 @@ ANON_FILE="highspeed_heudiconv_anonymizer.py"
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# make the anonymizer file executable:
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chmod +x "${PATH_CODE}/heudiconv/$ANON_FILE"
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# path to the directory where error and out path_logs of cluster jobs are saved:
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-PATH_LOGS="${PATH_BASE}/${PROJECT_NAME}/logs/heudiconv/$(date '+%Y%m%d_%H%M%S')"
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+PATH_LOGS="${PATH_PROJECT}/logs/heudiconv/$(date '+%Y%m%d_%H%M%S')"
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# path to the text file with all subject ids:
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-PATH_SUB_LIST="${PATH_CODE}/parameters/highspeed_participant_list.txt"
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+PATH_SUB_LIST="${PATH_CODE}/highspeed-participant-list.txt"
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# ==============================================================================
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# CREATE RELEVANT DIRECTORIES:
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# ==============================================================================
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-# create output directory:
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-if [ ! -d ${PATH_OUTPUT} ]; then
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- mkdir -p ${PATH_OUTPUT}
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- echo "created ${PATH_OUTPUT}"
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-fi
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# create directory for log files:
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if [ ! -d ${PATH_LOGS} ]; then
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mkdir -p ${PATH_LOGS}
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