From fd6f4cd0864460737170d2626de84209154b45a8 Mon Sep 17 00:00:00 2001 From: Joshua Newton Date: Mon, 30 Oct 2023 16:11:25 -0400 Subject: [PATCH] `batch_single_subject.sh`: Fix lumbar filenames --- single_subject/batch_single_subject.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh index e53aeb5..6cedc7d 100755 --- a/single_subject/batch_single_subject.sh +++ b/single_subject/batch_single_subject.sh @@ -218,9 +218,9 @@ sct_register_multimodal -i t1_crop.nii.gz -d ../t2/t2_crop.nii.gz -param step=1, cd ../t2_lumbar # Crop full-body image to isolate the lumbar region (lowest 200 axial slices) -sct_crop_image -i t2.nii.gz -zmax 200 +sct_crop_image -i t2.nii.gz -zmax 200 -o t2_lumbar.nii.gz # Use lumbar-specific `sct_deepseg` model to segment the spinal cord -sct_deepseg -i t2_crop.nii.gz -task seg_lumbar_sc_t2w +sct_deepseg -i t2_lumbar.nii.gz -task seg_lumbar_sc_t2w # Generate labels for the 2 spinal cord landmarks: cauda equinea ('99') and T9-T10 disc ('17') # Note: Normally this would be done manually using fsleyes' "Edit mode -> Create mask" functionality. (Uncomment below) @@ -229,12 +229,12 @@ sct_deepseg -i t2_crop.nii.gz -task seg_lumbar_sc_t2w # # However, since this is an automated script with example data, we will place the labels at known locations for the # sake of reproducing the results in the tutorial. -sct_label_utils -i t2.nii.gz -create 22,77,187,17:27,79,80,60 -o t2_crop_labels.nii.gz +sct_label_utils -i t2.nii.gz -create 22,77,187,17:27,79,80,60 -o t2_lumbar_labels.nii.gz # Register the image to the template using segmentation and labels -sct_register_to_template -i t2_crop.nii.gz \ - -s t2_crop_seg.nii.gz \ - -ldisc t2_crop_label.nii.gz \ +sct_register_to_template -i t2_lumbar.nii.gz \ + -s t2_lumbar_seg.nii.gz \ + -ldisc t2_lumbar_labels.nii.gz \ -c t2 -qc qc \ -param step=1,type=seg,algo=centermassrot:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=3,slicewise=0:step=3,type=im,algo=syn,metric=CC,iter=3,slicewise=0