fmri_processing_scripts/computeCensor at master · LabNeuroCogDevel/fmri_processing_scripts · GitHub

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#!/bin/bash
set -e
function printHelp() {

cat <<EndOfHelp
-----------------------------------
Script to compute motion censor for a given directory

   -dir         : directory to search for motion parameters
   -mfile       : name of raw motion parameters files (default = mcplots.par
   -censor_norm : euclidean norm for censoring motion (default = 0.9)

   Example: computeCensor -dir /gpfs/group/mnh5174/default/testdir -mfile mcplots.par -censor_norm 1.1
-----------------------------------
EndOfHelp

}

#END

#if no parameters are passed in, then print help and exit.
if [ $# -eq 0 ]; then
    printHelp
    exit 0
fi


ddir=
motraw="mcplots.par"
cens=0.9

while [ -n "$1" ]; do
    case $1 in
	-dir)           ddir="$2";        shift 2;;  # directory containing functional data
	-mfile)         motraw=$2;        shift 2;;  # filename for raw motion parameters: default to mcplots.par
	-censor_norm)   cens=$2;		  shift 2;;  # euclidean norm thrshold for censor
	*) echo -e "\n[Unrecognized option '$1']\n";
	    printHelp
	    exit 1;;
    esac
done

[[ -z "$ddir" || ! -d "$ddir" ]] && echo "Cannot locate directory: $ddir" && exit 1

#convert to absolute path to avoid problems with cd bewlo
ddir=$(echo $(cd "$ddir"; pwd) )

runfiles=$( find "${ddir}" -iname "$motraw" -type f )

for r in ${runfiles}; do

    fname=$( basename "$r" )
    fbase=$( echo "$fname" | sed 's/\.[^.]*$//' ) #strip off file extension
    rundir=$( dirname "$r" )

    cd "$rundir"
    echo -e "===\n  ${r}"

    #create first derivatives of motion (velocity)
    [ ! -r "${fbase}_velocity.par" ] && 1d_tool.py -overwrite -infile "$fname" -set_nruns 1 -derivative -write "${fbase}_velocity.par"

    #Demean the motion parameters
    [ ! -r "${fbase}_demeaned.1D" ] && 1d_tool.py -overwrite -infile "$fname" -set_nruns 1 -demean -write "${fbase}_demeaned.1D" -overwrite

    if [ ! -r "censor.1D" ]; then

	#afni's default call
	1d_tool.py -infile "$fname" -set_nruns 1 \
	    -show_censor_count -censor_prev_TR -overwrite \
	    -censor_motion $cens "${fbase}_censor"

	#censor TRs based on motion spikes
	#0,1,2 cols are rotation x,y,z; 3,4,5 cols are translation x,y,z.

        # numCensored=$(1d_tool.py \
        #     -infile ${subnum}_motion_all.par[3..5] \
        #     -set_nruns ${numRuns} \
        #     -derivative \
        #     -collapse_cols euclidean_norm \
	#     -extreme_mask -.8 .8 \
	#     -censor_prev_TR \
	#     -write_censor "${subnum}_censor.1D" \
	#     -write_CENSORTR "${subnum}_censorTR.txt" \
	#     -overwrite)
    fi

    echo -e "===\n"

    #rm -f mcplots_demeaned

done