From 0965ff5987965bc93108db62cceee25817250eb9 Mon Sep 17 00:00:00 2001
From: Tom <tom_bresser@hotmail.com>
Date: Tue, 27 Feb 2024 11:57:15 +0100
Subject: [PATCH] typo

---
 .../preprocess_topup_eddy_synb0.sh                        | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/structural_preprocessing/preprocess_topup_eddy_synb0.sh b/src/structural_preprocessing/preprocess_topup_eddy_synb0.sh
index 599a4e8..7fec827 100755
--- a/src/structural_preprocessing/preprocess_topup_eddy_synb0.sh
+++ b/src/structural_preprocessing/preprocess_topup_eddy_synb0.sh
@@ -60,7 +60,7 @@ parse_input()
         	shift 
                     ;;
    		--dwiFile=*)
-        	dwiFiles=${1#*=}
+        	dwiFile=${1#*=}
         	shift 		
         ;;
    		--dwiFiles=*)
@@ -165,7 +165,7 @@ brainMaskFile=${dwiProcessedFile/.nii.gz/_mask.nii.gz} # DO NOT CHANGE: HARDCODE
 topup -v --imain="$synb0File" --config=b02b0.cnf \
 --datain="$acqpFile" --out="${dwiProcessedFile/.nii.gz/}" \
 --iout="$dwiB0UnwarpedScansFile" --subsamp=1
-rm "${dwiB0ScansFile/.nii.gz/}".{nii.gz,topup_log}
+#rm "${dwiB0ScansFile/.nii.gz/}".{nii.gz,topup_log}
 
 
 # -------------------------------------
@@ -176,6 +176,10 @@ fslmaths "$dwiB0UnwarpedScansFile" -Tmean "$dwiReferenceFile"
 bet "$dwiReferenceFile" "$dwiProcessedFile" -m -n # creates $brainMaskFile
 rm "$dwiReferenceFile" "$dwiB0UnwarpedScansFile"
 
+# error check
+echo $dwiFile
+echo $dwiProcessedFile
+
 # Run eddy current correction on only the dwi data
 $eddyVersion -v --imain="$dwiFile" \
              --mask="$brainMaskFile" \