From 146a33f06c3720ed9a653c80275f2dafd30daa29 Mon Sep 17 00:00:00 2001 From: Julien Cohen-Adad Date: Tue, 7 Jun 2022 15:59:16 -0400 Subject: [PATCH] Clarified pipeline purpose about brain registration --- preprocessing/preprocess_data.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/preprocessing/preprocess_data.sh b/preprocessing/preprocess_data.sh index e1cf085..363bd98 100644 --- a/preprocessing/preprocess_data.sh +++ b/preprocessing/preprocess_data.sh @@ -90,6 +90,7 @@ sct_deepseg_sc -i ${file_ses2_onlyfile}_res.nii.gz -c t1 -o ${file_ses2_onlyfile # Perform registration ses-01 --> ses-02 # NOTE: We are passing the un-resampled / original ses-01 as the input to avoid double interpolation +# NOTE: We do NOT need to co-register the brain, because it was ALREADY co-registered by the MS-CHALLENGE team. sct_register_multimodal -i ${file_ses1}.nii.gz -iseg ${file_ses1_onlyfile}_seg.nii.gz -d ${file_ses2_onlyfile}_res.nii.gz -dseg ${file_ses2_onlyfile}_seg.nii.gz -o ${file_ses1_onlyfile}_reg.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=3 # Dilate spinal cord mask