Models:
Samuel Callahan
SCallahan/
pytorch-mri-segmentation
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[f2ca4d]: / registration_scripts (not used) / FLAIR_to_template.sh

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scriptDir="../../ANTs/"

template_fp="../../Data/Templates/mni_128x128x64.nii"

dataPath="../../Data/MS2017b/scans/*/"



for i in $(ls -d $dataPath);

do 

	FLAIR_fp=""$i"pre/FLAIR.nii.gz" && \

	WMH_fp=""$i"wmh.nii.gz" && \

	T1_fp=""$i"pre/T1.nii.gz" && \ 

	#create folder

	mkdir tempDir && \



	#copy FLAIR file to folder

	#cp $flair_fp tempDir



	$scriptDir/antsRegistrationSyNQuick.sh -d 3 -f $T1_fp -m $FLAIR_fp -o tempDir/out1 -t r && \

	$scriptDir/antsRegistrationSyNQuick.sh -d 3 -f $template_fp -m $T1_fp -o tempDir/out2 && \



	$scriptDir/antsApplyTransforms -d 3 -i $FLAIR_fp -o tempDir/FLAIR_s128.nii.gz -t tempDir/out10GenericAffine.mat -t tempDir/out20GenericAffine.mat -r tempDir/out21Warp.nii.gz -n BSpline

	$scriptDir/antsApplyTransforms -d 3 -i $WMH_fp -o tempDir/wmh_s128.nii.gz -t tempDir/out10GenericAffine.mat -t tempDir/out20GenericAffine.mat -r tempDir/out21Warp.nii.gz -n NearestNeighbor

	#out2Warp.nii.gz

	#out2GenericAffine.mat

	#out1GenericAffine.mat

	mv tempDir/FLAIR_s128.nii.gz ${i}pre/

	mv tempDir/wmh_s128.nii.gz ${i}



	rm -r tempDir

	#echo ${i};

done

#for loop

	#make directory

	#move files there

	#apply scripts

	#move created FLAIR file

	#delete directory





#"$scriptDir"/antsRegistrationSyNQuick.sh -d 3 -f 

#./antsRegistrationSyNQuick.sh -d 3 -f ../test/mni_icbm152_t1_tal_nlin_sym_09a.nii -m ../test/T1.nii.gz -o ../test/test

#./antsRegistrationSyNQuick.sh -d 3 -f ../test/T1.nii.gz -m ../test/FLAIR.nii.gz -o ../test/test2 -t r