[Brains-users] Script for clipping the brain and making all data a specified size reguardless of input image size.

[Hans Johnson]

Clipping Brain Images and Filling Background
The following is a script for clipping a brain from the skull and filling
the background of an image with "CSF" values. It is used for high
dimensional warping.
to be used via    brains2 -b scriptname
set wdir [ pwd ] 
set acpcdir [ getACPCdir $wdir ]
set mrqid [ getScanIdFromACPCdir $acpcdir ]
set suffix "segment_BOBF.hdr"
set aliases_filename "temp_aliases"
set closeoperator_mm 3
set thresholdvalue 70

set basedirname /raid1/data/methods/warp/BOBF_IPL_PET_MAPPING_I1_L1
set outfilename ${basedirname}/images/${mrqid}_${suffix}
set outfilename ${wdir}/${mrqid}_${suffix}
set filename ${basedirname}/data/$aliases_filename
set fileptr [  open ${filename} a  ]
puts ${fileptr} "S${mrqid} ${outfilename}"
close ${fileptr}
if { [  file isfile $outfilename  ] } {
   puts "File exists ($outfilename), exiting"
   exit 0
} else {
   set segPath [ getSegmentImageName $acpcdir ]
   #set t1Path [ getResampledT1ImageName $acpcdir ]
   set brainPath [ getBrainMaskName $acpcdir ]
   if { [  file isfile $segPath  ]  && [  file isfile $brainPath  ] } {
           puts "Processing files segmentedImage $segPath brainMask
$brainPath"
           set origseg [ b2 load image $segPath ]

           set origdims [ b2 get dims image $origseg ]
           set origres [ b2 get res image $origseg ]
           set newdims $origdims
           set newres $origres
           set tnsfm [ b2 create affine-transform $newdims $newres $origdims
$origres ]
           # This produced an identity affine transform.  Note:  to get
           # an inter-spatial identity transform, use the dims and res
           # you want to end up with for newdims and newres.
           if {$tnsfm == -1} {
             puts "Script halting: 'b2 create affine-transform' couldn't
handle dims list '$origdims' and res list '$origres'."
             exit 1
           }

           b2 set transform $tnsfm image $origseg

           set seg [ b2 resample image $origseg plane= coronal ]
           set origbrain [ b2 load mask $brainPath ]
           set brain [ b2 resample mask forward $origbrain $tnsfm ]

           b2 destroy image $origseg
           b2 destroy mask $origbrain

           set imageres 1.015625
           set closeoperator [ expr ${closeoperator_mm} / ${imageres} ]
           set closeoperator_max [ expr ${closeoperator} * 3.0 ]
           puts "close operator sizes $closeoperator ${closeoperator_max}"

           #set t1 [ b2 load image $t1Path ]
           set brainmask [ b2 erode mask $brain $closeoperator_max ]
           set thresholdmask [  b2 threshold image $seg $thresholdvalue  ]
           set tbmask [  b2 and masks $brain $thresholdmask  ]
           set errodemask [  b2 erode mask $tbmask $closeoperator  ]
           set dilatemask [  b2 dilate mask $errodemask $closeoperator  ]
           set filledmask [  b2 or masks  $dilatemask $brainmask ]
           set notmask [ b2 not mask $filledmask ]
           set backgroundimage [ b2 sum masks [ list $notmask $notmask ]  ]
           set clbgimage [ b2 clip image $backgroundimage $notmask  ]
           set csfbgimage [  b2 multiply images $clbgimage scale= [expr
${thresholdvalue}/2 ] data-type= unsigned-8bit  ]
           #set cut [ b2 clip image $t1 $filledmask ]
           set cut [ b2 clip image $seg $filledmask ]
           b2 hide every mask
           b2 destroy image $brain
           b2 destroy image $backgroundimage
           b2 destroy image $clbgimage
           set finalbigimage [ b2 sum images [ list $cut $csfbgimage ]  ]
           b2 destroy image $csfbgimage
           b2 destroy image $cut

           set finalimage $finalbigimage
           b2 save image ${outfilename} strictAnalyze75 $finalimage
data-type= unsigned-8bit plane= coronal
    } else {
           puts "ERROR ERROR ERROR: Missing necessary files segmentedImage
$segPath brainMask $brainPath from $wdir"
           exit -1
    }
}
b2 exit
--Hans 14:15, 26 Oct 2004 (CDT)