T1w and T2w age-grouped pediatric templates

Pediatric spinal cord templates generated for the following age groups : 10-12, 13-15 and 16-17.

Details on this release

Summary of template-generation

1. Data pre-processing

Data was first segmented using sct_deepseg with the contrast agnostic model v2.4 (SCT release 6.4). Manual corrections were done when necessary.

Vertebral labeling was then performed automatically using sct_label_vertebrae. For images where the automatic approach failed, the C2-C3 disc was manually labeled using sct_label_utils, and passing the resulting file to sct_label_vertebrae.

2. Data normalization

Data was normalized using preprocess_normalize.py .
Visual inspection of the straightened images was performed to ensure all images were adequate for template generation.

3. Template generation

Templates were generated for all three age groups separately, using generate_template.py on an Alliance Canada cluster with 10 CPUs per task and 3G of memory per CPU core. The template generation was stopped after 12 iterations.

Current templates

The current T1w and T2w templates were generated for each age group (10-12, 13-15 and 16-17), using the following number of participants :

Age groups	T1w template	T2w template
10-12	14	10
13-15	18	21
16-17	18	13

The templates cover the spinal cord from C2 to T11.

T1w and T2w pediatric templates

Initial templates generated the structural MRI data of 18 pediatric subjects. The T1w and T2w templates were created separately and averaging was stopped after 11 iterations. Both the templates are In the same voxel and world space coordinates.

Details on this release

Summary of template-generation:

1. An initial template space is generated based on the average length of the intervertebral levels of the subjects in the dataset of interest. It gets saved downstream as a file called template_mask.mnc.

2. The straightening and normalization method straightens all of the spinal cord images of the subjects (i.e. from both T1w and T2w) and brings them into the same space as template_mask.mnc.

3. An iterative vowel-wise inter-subject averaging begins.

Current templates

1. An initial template space is generated based on the average length of the intervertebral levels of the subjects in the dataset of interest. It gets saved downstream as a file called template_mask.mnc. CHECKPOINT 1:

   • For the T1w images of the pediatric dataset, template_mask.mnc has xyz dimensions 201 x 201 x 688.
   • For the T2w images of the pediatric dataset, template_mask.mnc has xyz dimensions 201 x 201 x 688.

2. The straightening and normalization method straightens all of the spinal cord images of the subjects and brings them into the same space as template_mask.mnc.

   • For the T1w images of the pediatric dataset, all of the straightened images have xyz dimensions 201 x 201 x 688.
   • For the T2w images of the pediatric dataset, all of the straightened images have xyz dimensions 201 x 201 x 688.

3. The iterative vowel-wise inter-subject averaging begins.

   • For the T1w images of the pediatric dataset, this outputs a file (saved as pediatric-template_T1w.nii.gz after 8 iterations) with dimensions 201 x 201 x 688.
   • For the T2w images of the pediatric dataset, this outputs a file (saved as pediatric-template_T2w.nii.gz after 8 iterations) with dimensions 201 x 201 x 688.

Corrected Initial T1w and T2w pediatric templates

Initial templates generated the structural MRI data of 18 pediatric subjects. The T1w and T2w templates were created separately and averaging was stopped after 8 iterations.

Details on this release

Summary of template-generation (repeated from comment above)

1. An initial template space is generated based on the average length of the intervertebral levels of the subjects in the dataset of interest. It gets saved downstream as a file called template_mask.mnc.

2. The straightening and normalization method straightens all of the spinal cord images of the subjects and brings them into the same space as template_mask.mnc.

3. An iterative vowel-wise inter-subject averaging begins.

Current templates + previous error explained

1. An initial template space is generated based on the average length of the intervertebral levels of the subjects in the dataset of interest. It gets saved downstream as a file called template_mask.mnc. CHECKPOINT 1:

   • For the T1w images of the pediatric dataset, template_mask.mnc has xyz dimensions 201 x 201 x 688.
   • For the T2w images of the pediatric dataset, template_mask.mnc has xyz dimensions 201 x 201 x 680.

2. The straightening and normalization method straightens all of the spinal cord images of the subjects and brings them into the same space as template_mask.mnc.

   • For the T1w images of the pediatric dataset, all of the straightened images have xyz dimensions 201 x 201 x 688.
   • For the T2w images of the pediatric dataset, all of the straightened images have xyz dimensions 201 x 201 x 680.
   • ERROR EXPLAINED: The reason why this was not the case prior was due to an error on my part: the straightening and normalization has to be performed on ALL of the subjects at once such that template_mask.mnc is generated correctly. I originally performed the straightening and normalization in batches, meaning that the dimensions of template_mask.mnc were not based on an average across all subejcts. Is this clear?

3. The iterative vowel-wise inter-subject averaging begins.

   • For the T1w images of the pediatric dataset, this outputs a file (saved as pediatric-template_T1w.nii.gz after 8 iterations) with dimensions 201 x 201 x 688.
   • For the T2w images of the pediatric dataset, this outputs a file (saved as pediatric-template_T2w.nii.gz after 8 iterations) with dimensions 201 x 201 x 680.

Initial T1w and T2w pediatric templates

Initial templates generated the structural MRI data of 18 pediatric subjects. The T1w and T2w templates were created separately and averaging was stopped after 7 iterations.