Merge pull request #3 from smoia/Remove-initial-resampling

Removing 3drefit and 3dresample calls after a chat with @oesteban
smoia · Oct 21, 2021 · c020c52 · c020c52
2 parents 2c4c872 + 29746b7
commit c020c52
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Showing 2 changed files with 2 additions and 12 deletions.
diff --git a/01.anat_preproc/01.anat_correct.sh b/01.anat_preproc/01.anat_correct.sh
@@ -65,15 +65,10 @@ cd ${adir} || exit 1
 anat=$( basename ${anat_in%.nii.gz} )
 if_missing_do mkdir ${tmp}
 
-# 01. Deoblique & resample
-echo "Resample ${anat}"
-3drefit -deoblique ${anat_in}.nii.gz 
-3dresample -orient RPI -inset ${anat_in}.nii.gz -prefix ${tmp}/${anat}_RPI.nii.gz -overwrite
-
 ## 02. Bias Field Correction with ANTs
 # 02.1. Truncate (0.01) for Bias Correction
 echo "Performing BFC on ${anat}"
-ImageMath 3 ${tmp}/${anat}_trunc.nii.gz TruncateImageIntensity ${tmp}/${anat}_RPI.nii.gz 0.02 0.98 256
+ImageMath 3 ${tmp}/${anat}_trunc.nii.gz TruncateImageIntensity ${anat_in}.nii.gz 0.02 0.98 256
 # 02.2. Bias Correction
 N4BiasFieldCorrection -d 3 -i ${tmp}/${anat}_trunc.nii.gz -o ${tmp}/${anat}_bfc.nii.gz
 

diff --git a/02.func_preproc/01.func_correct.sh b/02.func_preproc/01.func_correct.sh
@@ -78,12 +78,7 @@ then
 	fslroi ${funcsource} ${tmp}/${func}_dsd.nii.gz ${voldiscard} -1
 	funcsource=${tmp}/${func}_dsd
 fi
-# 01.2. Deoblique & resample
-echo "Deoblique and RPI orient ${func}"
-3drefit -deoblique ${funcsource}.nii.gz
-3dresample -orient RPI -inset ${funcsource}.nii.gz -prefix ${tmp}/${func}_RPI.nii.gz -overwrite
-# set name of source for 3dNwarpApply
-funcsource=${tmp}/${func}_RPI
+
 # 01.3. Compute outlier fraction if there's more than one TR
 if [[ "${nTR}" -gt "1" ]]
 then