preproc_shFiles/make_grayplots.sh at master · SpragueLab/preproc_shFiles · GitHub

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#!/bin/bash
# make_grayplots.sh
#
# Runs AFNI's 3dGrayplot function on all run??.nii.gz files within specified $PROJECT/$SUBJ/$SESS directory and saves pngs in specified $PROJECT/$SUBJ/align_QC/$SUBJ_$SESS_run??_grayplot.png
#
# Assumes typical (~2019-2021) Sprague lab directory structure - PROJECT/SUBJ/SESS/
#
# INPUTS:
#   - PROJECT: project directory
#   - SUBJ:    subject ID
#   - SESS:    session name
#
# OUTPUTS:
#   - saves a .png file as produced in AFNI's 3dGrayplot function as: $DATAROOT/$PROJECT/$SUBJ/align_QC/$SUBJ_$SESS_run??_grayplot.png
#
# assumes you have a DATAROOT environment variable that says where project directories live
#
# TC Sprague 11/7/2021

EXPTDIR=$1
SUBJ=$2
SESS=$3

# size of image to be saved
XDIM=2560
YDIM=1440


# where files are found
NIIFILES=$DATAROOT/$EXPTDIR/$SUBJ/$SESS/run??.nii.gz

# where to save files
OUTDIR=$DATAROOT/$EXPTDIR/$SUBJ/align_QC
OUTSUF=_grayplot.png

for thisfile in $NIIFILES
do
    echo "Making grayplot of: $thisfile"

    # do some bash stuff (based on stackoverflow answers...) to cut the path and extension from the filename
    tmprun="${thisfile##*/}"
    tmprunnum="${tmprun%%.*}"

    3dGrayplot -prefix $OUTDIR/${SUBJ}_${SESS}_${tmprunnum}$OUTSUF -dimen $XDIM $YDIM -input $thisfile

done