From 07bd03d9234ba406f31666ba7817456728d12127 Mon Sep 17 00:00:00 2001 From: Joshua Newton Date: Fri, 6 Dec 2024 14:44:11 -0500 Subject: [PATCH] `batch_single_subject.sh`: Add TSNR QC commands --- single_subject/batch_single_subject.sh | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh index a7c15c8..e678866 100755 --- a/single_subject/batch_single_subject.sh +++ b/single_subject/batch_single_subject.sh @@ -349,6 +349,13 @@ sct_create_mask -i fmri.nii.gz -p centerline,t2_seg_reg.nii.gz -size 35mm -f cyl # Motion correction (using mask) sct_fmri_moco -i fmri.nii.gz -m mask_fmri.nii.gz -qc ~/qc_singleSubj -qc-seg t2_seg_reg.nii.gz +# Cord segmentation on motion-corrected averaged time series +sct_deepseg -i fmri_moco_mean.nii.gz -task seg_sc_contrast_agnostic -qc ~/qc_singleSubj/ +# TSNR before/after motion correction with QC report +sct_fmri_compute_tsnr -i fmri.nii.gz +sct_fmri_compute_tsnr -i fmri_moco.nii.gz +sct_qc -i fmri_tsnr.nii.gz -d fmri_moco_tsnr.nii.gz -s fmri_moco_mean_seg.nii.gz -p sct_fmri_compute_tsnr -qc ~/qc_singleSubj/ + # Register the template to the fMRI scan. # Note: here we don't rely on the segmentation because it is difficult to obtain one automatically. Instead, we rely on # ANTs_SyN superpower to find a suitable transformation between the PAM50_t2 and the fMRI scan. We don't want to