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map_to_fsaverage_parallel.bash
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map_to_fsaverage_parallel.bash
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#!/bin/bash
# map_to_fsaverage_parallel.bash -- run stuff in parallel over a number of subjects.
# By default, maps measures to fsaverage using the map_to_fsaverage_single_subject.bash inner cargo script.
# (E.g., subject/surf/lh.pial_lgi -> subject/surf/lh.pial_lgi.fwhmX.fsaverage.mgh for several X)
#
######################### IMPORTANT #############################
# Adapt the JOB SETTINGS at the end of this file to configure #
# the command to run for each of the subject! #
######################### IMPORTANT #############################
#
# Written by TS
## For more details on the <rename_only> argument, see the map_to_fsaverage_single_subject.bash script.
APPTAG="[MAP_PAR]"
##### General settings #####
# Number of consecutive GNU Parallel jobs. Note that 0 for 'as many as possible'. Maybe set something a little bit less than the number of cores of your machine if you want to do something else while it runs.
# See 'man parallel' for details.
NUM_CONSECUTIVE_JOBS="$3"
if [ -z "$NUM_CONSECUTIVE_JOBS" ]; then
NUM_CONSECUTIVE_JOBS=22
echo "$APPTAG Number of parallel jobs not specified on command line, defaulting to $NUM_CONSECUTIVE_JOBS jobs."
fi
###### End of job settings #####
## Check some stuff
# SUBJECTS_DIR must be set
if [ -z "${SUBJECTS_DIR}" ]; then
echo "$APPTAG WARNING: Environment variable SUBJECTS_DIR not set. Exiting."
exit 1
fi
# By default, SUBJECTS_DIR gets set to the FreeSurfer subjects folder, but that makes no sense unless you want to work on example data.
if [ -d "${SUBJECTS_DIR}/bert" ]; then # 'bert' is a FreeSurfer example subject.
echo "$APPTAG WARNING: Environment variable SUBJECTS_DIR seems to point at the subjects dir of the FreeSurfer installation: '${SUBJECTS_DIR}'. Configure it to point at your data!"
echo "$APPTAG NOTE: You can ignore the last warning if you have a subject named 'bert' in your study."
fi
# When ppl install FreeSurfer on a new machine, it is a common error to forgot about the license file you have to manually copy into the installation dir.
# When the file is missing, FreeSurfer will refuse to work and all jobs in the parallel run will die.
# You can get a license.txt file for free by registering on the FreeSurfer website.
if [ ! -f "${FREESURFER_HOME}/license.txt" ]; then
echo "$APPTAG ERROR: The FreeSurfer license file was not found at '${FREESURFER_HOME}/license.txt'. Run would fail, exiting now. (Get a free license on the Freesurfer website and copy it to that dir to fix this error.)"
exit 1
fi
if [ -n "$1" ]; then
SUBJECTS_FILE="$1"
## Check for given subjects file.
if [ ! -f "$SUBJECTS_FILE" ]; then
echo "$APPTAG ERROR: Subjects file '$SUBJECTS_FILE' not found."
exit 1
fi
else
echo "$APPTAG ERROR: Must specify subjects_file. Exiting. (This is a text file with 1 subject per line.)"
echo "$APPTAG Usage: $0 <subjects_file> <measure> [[[[<num_proc>] <template_subject>] <force>] <rename_only>]"
echo "$APPTAG <subjects_file> : path to a textfile containing one subject per line"
echo "$APPTAG <measure> : the measure to map to fsaverage, e.g., 'thickness', 'curv', or 'truncation'."
echo "$APPTAG <num_proc> : number of processes (subjects) to run in parallel. Set to 0 for max for your machine."
echo "$APPTAG <template_subject> : Optional, the template subject to map data to. Defaults to fsaverage."
echo "$APPTAG <force> 'YES' or 'NO', whether to re-map the data even if the ouput files already exist. Defaults to 'NO'."
echo "$APPTAG <rename_only> 'YES' or 'NO', whether to rename the files only and convert to MGH. See script for details. Defaults to 'NO'."
echo "$APPTAG * Note that the environment variable SUBJECTS_DIR must also be set correctly."
echo "$APPTAG The SUBJECTS_DIR is set to: '$SUBJECTS_DIR'."
exit 1
fi
FORCE="NO"
if [ -n "$5" ]; then
FORCE="$5"
fi
RENAME_ONLY="NO"
if [ -n "$6" ]; then
RENAME_ONLY="$6"
fi
# Check for borken line endings (Windows line endings, '\r\n') in subjects.txt file, a very common error.
# This script can cope with these line endings, but we still warn the user because other scripts may choke on them.
NUM_BROKEN_LINE_ENDINGS=$(grep -U $'\015' "${SUBJECTS_FILE}" | wc -l | tr -d '[:space:]')
if [ $NUM_BROKEN_LINE_ENDINGS -gt 0 ]; then
echo "$APPTAG WARNING: Your subjects file '${SUBJECTS_FILE}' contains $NUM_BROKEN_LINE_ENDINGS incorrect line endings (Windows style line endings)."
echo "$APPTAG WARNING: (cont.) While this script can work with them, you will run into trouble sooner or later, and you should definitely fix them (use the 'tr' command or a proper text editor)."
fi
SUBJECTS=$(cat "${SUBJECTS_FILE}" | tr -d '\r' | tr '\n' ' ') # fix potential windows line endings (delete '\r') and replace newlines by spaces as we want a list
SUBJECT_COUNT=$(echo "${SUBJECTS}" | wc -w | tr -d '[:space:]')
echo "$APPTAG Parallelizing over the ${SUBJECT_COUNT} subjects in file '${SUBJECTS_FILE}' using ${NUM_CONSECUTIVE_JOBS} threads."
# We can check already whether the subjects exist.
for SUBJECT in $SUBJECTS; do
if [ ! -d "${SUBJECTS_DIR}/${SUBJECT}" ]; then
echo "$APPTAG ERROR: Directory for subject '${SUBJECT}' not found in SUBJECTS_DIR '${SUBJECTS_DIR}'. Exiting."
exit 1
fi
done
################### JOB SETTINGS -- adjust this ##################
#echo ${SUBJECTS} | tr ' ' '\n' | parallel "echo {}" # Debug: This only print one subject per line.
## The full command that will be run for each subject. The {} will be replaced by the subject id. You could get additional args from whereever and add them (e.g., from $2 .. $n of this script. Keep in mind that $1 is already in use!).
## Feel free to use shell syntax to do stuff in the command.
## Here, we use another argument from the command line of this script:
if [ -z "$2" ]; then
echo "$APPTAG ERROR: Must specify subjects_file. Exiting. (This is a text file with 1 subject per line.)"
echo "$APPTAG Usage: $0 <subjects_file> <measure> [[[[<num_proc>] <template_subject>] <force>] <rename_only>]"
echo "$APPTAG <subjects_file> : path to a textfile containing one subject per line"
echo "$APPTAG <measure> : the measure to map to fsaverage, e.g., 'thickness', 'curv', or 'truncation'."
echo "$APPTAG <num_proc> : number of processes (subjects) to run in parallel. Set to 0 for max for your machine."
echo "$APPTAG <template_subject> : Optional, the template subject to map data to. Defaults to fsaverage."
echo "$APPTAG <force> 'YES' or 'NO', whether to re-map the data even if the ouput files already exist. Defaults to 'NO'."
echo "$APPTAG <rename_only> 'YES' or 'NO', whether to rename the files only and convert to MGH. See script for details. Defaults to 'NO'."
echo "$APPTAG * Note that the environment variable SUBJECTS_DIR must also be set correctly."
echo "$APPTAG The SUBJECTS_DIR is set to: '$SUBJECTS_DIR'."
exit 1
else
MEASURE="$2"
fi
TEMPLATE_SUBJECT="fsaverage"
if [ -n "$4" ]; then
TEMPLATE_SUBJECT="$4"
fi
echo "$APPTAG Using template subject '${TEMPLATE_SUBJECT}'."
if [ ! -d "${SUBJECTS_DIR}/${TEMPLATE_SUBJECT}" ]; then
echo "$APPTAG ERROR: Directory for template subject '${TEMPLATE_SUBJECT}' not found in SUBJECTS_DIR '${SUBJECTS_DIR}'. Exiting."
exit 1
fi
EXEC_PATH_OF_THIS_SCRIPT=$(dirname $0)
CARGO_SCRIPT="${EXEC_PATH_OF_THIS_SCRIPT}/map_to_fsaverage_single_subject.bash"
if [ ! -x "${CARGO_SCRIPT}" ]; then
echo "$APPTAG ERROR: Cargo script at ${CARGO_SCRIPT} not found or not executable. Check path and/or run 'chmod +x <file>' on it to make it executable. Exiting."
exit
fi
echo "$APPTAG Mapping measure $MEASURE to $TEMPLATE_SUBJECT for $SUBJECT_COUNT subjects in dir $SUBJECTS_DIR using $NUM_CONSECUTIVE_JOBS $cores."
############ execution, no need to mess with this. ############
DATE_TAG=$(date '+%Y-%m-%d_%H-%M-%S')
echo ${SUBJECTS} | tr ' ' '\n' | parallel --jobs ${NUM_CONSECUTIVE_JOBS} --workdir . --joblog LOGFILE_MAP_PARALLEL_${DATE_TAG}.txt "$CARGO_SCRIPT {} $MEASURE $TEMPLATE_SUBJECT $FORCE $RENAME_ONLY"