Create mean image across large number of subject for validation

[sandrinebedard]

Description

To validate the accuracy of the registration to the template using the spinal nerve dorsal rootlets compared to the discs, we will create a mean image across the Spine-Generic data-multi-subject dataset and see if we can better visualize the rootlets compared to the mean image using the intervertabral discs for registration to the template.

Method:

• SCT branch: sct_register_to_template.py
• Data: data-multi-subject
• Processing script: process_spine_generic.sh
• Script to average: average_images.py
• Add mid-points and updated info_list.txt in PAM50 data

Subjects that had missing rootlets levels were excluded: exclude_spine_generic.yml

You need to have this repository located under ~/code/

Launch processing command:

sct_run_batch -jobs 5 -script process_spine_generic.sh -path-data ~/datasets/data-multi-subject/derivatives/data_preprocessed/ -path-out <PATH_RESULTS>

Average images toghether

Average rootlets-based ana2template.nii.gz:

python average_images.py -path-data ~/processed_data/results_spine-generic_sub-amu01_rootlets_2024-10-18/data_processed -path-out ~/processed_data/results_spine-generic_sub-amu01_rootlets_2024-10-18/results/ -exclude processing_script/exclude_spine_generic.yml -path-file reg_rootlets

Average discs-based anat2template.nii.gz:

python average_images.py -path-data ~/processed_data/results_spine-generic_sub-amu01_rootlets_2024-10-18/data_processed -path-out ~/processed_data/results_spine-generic_sub-amu01_rootlets_2024-10-18/results/ -exclude processing_script/exclude_spine_generic.yml -path-file reg_discs

[sandrinebedard]

Results of mean image of anat2template.nii.gz of n=253:

Rootlets vs. PAM50

Discs vs. PAM50

Discs vs . Rootlets

Rootlets-regmean across n=253

Discs-reg mean across n=253

[jcohenadad]

omg this is beautiful! the "Discs vs . Rootlets" is 'cover journal' material