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mirecc:mireccanat:makefirst_anat

makeFirstAnat.sh Example Script:

the following is an example script that will convert your raw anatomical image (with bxh header) into LAS orientation, and into nifti format.

#!/bin/bash 
 
SUBJ=$1 
ANATDIR=~/path/to/raw/data/$SUBJ 
 
FSLDATADIR=/path/to/put/converted/anat/$SUBJ/rawdata 
SEGDIR=/path/to/segmentation/dir/$SUBJ/firstSeg 
 
#### make the directories if they do not exist 
mkdir -p $FSLDATADIR  
mkdir -p $SEGDIR 
 
#### converts anatomical to LAS #### 
bxhreorient --orientation=LAS $ANATDIR/series${2}/*bxh $FSLDATADIR/T1.bxh 
bxh2analyze -s --niigz $FSLDATADIR/T1.bxh $SEGDIR/T1_las 
 
#### creates a neck mask for running first, may need to change dimensions 
fslmaths $SEGDIR/T1_flip -roi 0 256 0 256 30 136 0 1 $SEGDIR/neckMask  
to run the script:
 
bash -x makeFirstAnat SUBJ# SERIES# 
mirecc/mireccanat/makefirst_anat.txt · Last modified: 2014/08/04 16:03 (external edit)