diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh index 7185b8e..7b2bc34 100755 --- a/single_subject/batch_single_subject.sh +++ b/single_subject/batch_single_subject.sh @@ -130,6 +130,19 @@ fsleyes t2.nii.gz -cm greyscale t2_sc_seg.nii.gz -cm red -a 70.0 t2_lesion_seg.n # 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 + + +# Rootlets segmentation +# ====================================================================================================================== +cd ../t2 +# Segment the spinal nerve rootlets +sct_deepseg -i t2.nii.gz -task seg_spinal_rootlets_t2w -qc ~/qc_singleSubj + +# Check results using Fsleyes +fsleyes t2.nii.gz -cm greyscale t2_seg.nii.gz -cm subcortical -a 70.0 & + + + # Registering T2 data to the PAM50 template # ====================================================================================================================== cd ../t2 diff --git a/tutorial-datasets.csv b/tutorial-datasets.csv index 22ae753..08c3304 100644 --- a/tutorial-datasets.csv +++ b/tutorial-datasets.csv @@ -41,6 +41,7 @@ data_processing-fmri-data,single_subject/data/fmri/fmri.nii.gz data_processing-fmri-data,single_subject/data/t2/t2.nii.gz data_processing-fmri-data,single_subject/data/t2s/warp_template2t2s.nii.gz data_processing-fmri-data,single_subject/data/t2s/warp_t2s2template.nii.gz +data_rootlets-segmentation,single_subject/data/t2/t2.nii.gz data_spinalcord-smoothing,single_subject/data/t1/t1.nii.gz data_spinalcord-smoothing,single_subject/data/t1/t1_seg.nii.gz data_visualizing-misaligned-cords,single_subject/data/t1/t1.nii.gz