forked from tommysprague/preproc_shFiles
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathprep_anat.sh
49 lines (32 loc) · 2.24 KB
/
prep_anat.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
#!/bin/bash
# prep_anat.sh
#
# Use this to set up symlink to processed freesurfer directory, and create surfanat files
# used for retinotopy. Run once per subj folder within an expt directory (not for each sess)
#
# Requires a pre-processed file already (need to sample on that grid)
#DATAROOT=/deathstar/data
EXPTDIR=$1
SUBJ=$2
ANATSUBJ=${SUBJ}anat
SESS=$3
# make symlink to freesurfer directory
#ln -s ../../fs_subjects/$ANATSUBJ $EXPTDIR/$SUBJ/$ANATSUBJ
# first preproc directorY: ls -d KD_RF1_r*_SEalign.results | head -1
# make surfanat files in $EXPTDIR/$SUBJ
#PREPROC_DIR=$(ls -d $EXPTDIR/$SUBJ/*/${SUBJ}_*r*_SEalign.results | head -1)
PREPROC_DIR=$(ls -d $DATAROOT/$EXPTDIR/$SUBJ/$SESS/${SUBJ}_*r*_SEalign.results | head -1)
PREPROC_IMG=$(ls $PREPROC_DIR/pb02.*.volreg+orig.BRIK* | head -1)
3dresample -prefix $DATAROOT/$EXPTDIR/$SUBJ/surfanat_brainmask_master.nii.gz -master $PREPROC_IMG -rmode Cu -overwrite -inset $DATAROOT/$EXPTDIR/$SUBJ/$ANATSUBJ/SUMA/brainmask.nii
3dresample -prefix $DATAROOT/$EXPTDIR/$SUBJ/surfanat_brainmask_master.nii.gz -orient rai -overwrite -inset $DATAROOT/$EXPTDIR/$SUBJ/surfanat_brainmask_master.nii.gz
#3dresample -prefix $EXPTDIR/$SUBJ/surfanat_brainmask_master_25mm.nii.gz -master $PREPROC_IMG -rmode Cu -inset $SUBJECTS_DIR/$ANATSUBJ/SUMA/brainmask.nii
# for computing in-plane resolution for _hires.nii.gz
# RESULT=$(echo "$MYVAR/2" | bc -l)
# extract the (square) voxel resolution from the surfanat_brainmask_master.nii.gz file
MYRES=$( 3dinfo -adi $DATAROOT/$EXPTDIR/$SUBJ/surfanat_brainmask_master.nii.gz )
# for vista expectations, we want the surfanat_brainmask_hires.nii.gz file to have xyz dimensions of 0.5, 0.5, 1 x MYRES, respectively
# the below will do the floating point math to get us there
HIRES=$(echo "$MYRES/2" | bc -l)
#3dresample -prefix $DATAROOT/$EXPTDIR/$SUBJ/surfanat_brainmask_hires.nii.gz -dxyz 1.0 1.0 2.0 -rmode Cu -orient RAI -inset $DATAROOT/$EXPTDIR/$SUBJ/surfanat_brainmask_master.nii.gz
3dresample -prefix $DATAROOT/$EXPTDIR/$SUBJ/surfanat_brainmask_hires.nii.gz -dxyz $HIRES $HIRES $MYRES -rmode Cu -orient RAI -overwrite -inset $DATAROOT/$EXPTDIR/$SUBJ/surfanat_brainmask_master.nii.gz
3dcopy -overwrite $DATAROOT/$EXPTDIR/$SUBJ/$ANATSUBJ/SUMA/T1.nii $DATAROOT/$EXPTDIR/$SUBJ/anat_T1_brain.nii