From 9ce002c68e7cae16c4e34ed4443cd005ee61356d Mon Sep 17 00:00:00 2001 From: valosekj Date: Mon, 16 Sep 2024 14:15:02 -0400 Subject: [PATCH] batch_single_subject.sh: add QC and Fsleyes command for the lesion analysis section --- single_subject/batch_single_subject.sh | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh index 997d593..7b2bc34 100755 --- a/single_subject/batch_single_subject.sh +++ b/single_subject/batch_single_subject.sh @@ -119,11 +119,14 @@ sct_compute_compression -i t2_compressed_seg.nii.gz -vertfile t2_compressed_seg_ cd ../t2_lesion # Segment the spinal cord and intramedullary lesion using the SCIsegV2 model # Note: t2.nii.gz contains a fake lesion for the purpose of this tutorial -sct_deepseg -i t2.nii.gz -task seg_sc_lesion_t2w_sci +sct_deepseg -i t2.nii.gz -task seg_sc_lesion_t2w_sci -qc ~/qc_singleSubj # Note: Two files are output: # - t2_sc_seg.nii.gz: the spinal cord segmentation # - t2_lesion_seg.nii.gz: the lesion segmentation +# Check results using Fsleyes +fsleyes t2.nii.gz -cm greyscale t2_sc_seg.nii.gz -cm red -a 70.0 t2_lesion_seg.nii.gz -cm blue-lightblue -a 70.0 & + # Compute various morphometric measures, such as number of lesions, lesion length, lesion volume, etc. sct_analyze_lesion -m t2_lesion_seg.nii.gz -s t2_sc_seg.nii.gz -qc ~/qc_singleSubj