==== 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.


<code bash>
#!/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 
</code>

== to run the script: ==

<code>
bash -x makeFirstAnat SUBJ# SERIES#
</code>