Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add data and commands for rootlets-segmentation tutorial #22

Merged
merged 2 commits into from
Oct 7, 2024
Merged

Add data and commands for rootlets-segmentation tutorial #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
aff4e4c
tutorial-datasets.csv: Update with rootlets data
valosekj Sep 16, 2024
d9768b2
batch_single_subject.sh: Update with rootlets segmentation
valosekj Sep 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 13 additions & 0 deletions single_subject/batch_single_subject.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
1 change: 1 addition & 0 deletions tutorial-datasets.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down