[Bug]: Registration issues

[elenaki94]

Have you checked original image orientation?

• I have verified that my images are properly oriented

Describe the bug

Hello RABIES team,

I tried to run preprocessing for one of my rat scans, but it seems that something goes wrong during the registration process, especially since when checking the QC reports, some parts look very weird. I have attached all the pictures from the QC folder and the workflow log, along with a screenshot of my anatomical image on ITK-SNAP.
I am worried there is a mismatch at the field of view between my images and the template. Could you let me know if I can fix something?

RABIES version

v0.5.5 (nightly)

Execution method

Docker

Operating system

windows wsl2 (ubuntu)

System specifications (optional)

CPU: 8 cores
RAM: 16 GB
Docker version: v29.2.0

RABIES command

docker run -it --rm -v C:\Users\nikalexi\Desktop\Fear_Conditioning_Rabies_analysis:/input_BIDS:ro -v C:\Users\nikalexi\Desktop\Fear_Conditioning_Rabies_analysis\preprocess_outputs:/preprocess_outputs ghcr.io/cobralab/rabies:nightly -p MultiProc preprocess /input_BIDS /preprocess_outputs --apply_STC --TR 1.2 --commonspace_reg masking=true,brain_extraction=false,template_registration=SyN,fast_commonspace=false

Log file

rabies_preprocess.log

QC report

Is the bug reproducible?

Not sure

Additional context

[Gab-D-G]

Hello @elenaki94 , thank you for providing all the visual reports, this helps.

I can tell right away that you are using the default mouse template for registration, so basically you are trying to register a large rat brain onto a small mouse brain. You will need to provide a rat template and associated mask files manually during preprocessing. You could check the SIGMA or Fischer template for instance.

Best,
Gabriel