template building/additional segmentations

[Javiercbr]

Hey there 👋

I’m trying to use FireANTs for full-body CT template building and ran into a problem with saving additional segmentations.

I set up my config as shown in the README, with a save_additional block like:

image_list_file: /media/SHARED/Corregistro/Pruebas_FireAnts/TemplateBuilding/lista_NVM.txt
image_prefix: null
image_suffix: null
num_subjects: null  

save_additional: 
  image_file:   ['/media/SHARED/Corregistro/Pruebas_FireAnts/TemplateBuilding/lista_NVM_TS.txt'] 
  image_prefix: ['label_']
  image_suffix: ['.nii.gz']
  is_segmentation: [true]

lista_NVM.txt and lista_NVM_TS.txt are mirror list files with the filenames of CT and the corresponding segmentation — they only differ in a string (CT instead of TS).

…but nothing happens — no extra images are saved.

I checked fireants/scripts/template/build_template.py and couldn’t find any place where save_additional is actually called or processed. It looks like the option exists in the configs, but the functionality might not have been wired into the script yet.

Is save_additional some kind of WIP or I’m missing something?

Thanks a lot!

[Javiercbr]

I'm sorry. I've just realised that you flagged it as WIP.

[rohitrango]

Yes, I was not sure what kind of formatting would be easiest for a user to provide additional labels.
I'm thinking that image_file can point to a csv/txt file similar to the image_list_file parameter with appropriate prefix and suffix, but parsing is_segmentation parameter for each possible image is tricky / can make user experience cumbersome. Let me know if you have any ideas here

[Javiercbr]

I can see several possible approaches:

• A configurable global flag that applies to every image listed in image_list_file
• Encoding a segmentation indicator directly in the filename, for example using a prefix like 'label_'
• Or, if neither of the above fits, adding an explicit is_segmentation field to image_list_file

[nimzodisaster]

Just wanted to jump in here to add that it would also be nice to provide the final registration transforms to the template