SIGMA Rat Brain Template and Atlas Substitution

[hookeba]

Hello Everyone!

I would like to substitute the SIGMA rat brain template and atlas for my resting-state fMRI analysis. I assume that I need to define the following commonspace template and associated mask/label files to override the mouse DSURQE defaults:

1. --anat_template
2. --brain_mask
3. --WM_mask
4. --CSF_mask
5. --labels

Unfortunately, when defining the --anat_template variable, I received the below error message. I am running Ubuntu 24.04.3 LTS with Python 3.7.11. Your help is greatly appreciated!

Brad

Traceback (most recent call last):
File "/home/rabies/miniforge/bin/rabies", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/home/rabies/RABIES/scripts/rabies", line 3, in
execute_workflow()
File "/home/rabies/RABIES/rabies/run_main.py", line 44, in execute_workflow
workflow = preprocess(opts, log)
File "/home/rabies/RABIES/rabies/run_main.py", line 179, in preprocess
raise ValueError(f"--anat_template file {opts.anat_template} doesn't exists.")
ValueError: --anat_template file /home/rabies/SIGMA_InVivo_Anatomical_Brain_template.nii.gz doesn't exists.

[Gab-D-G]

Hello,
Are you using a container? Can i have your full command line? The path you provided does not match an existing file either in the container if you are using one, or in your computer.

[hookeba]

Hello Gabriel!

I am using Docker 29.13. Here is my command line:

docker run -it --rm --user $(id -u) -v $PWD/input_BIDS:/input_BIDS:ro -v $PWD/preprocess_outputs:/preprocess_outputs/ gabdesgreg/rabies:latest -p MultiProc preprocess /input_BIDS/ /preprocess_outputs/ --apply_STC --TR 1.0 --commonspace_reg masking=true,brain_extraction=false,template_registration=SyN,fast_commonspace=false --anat_template

I am not certain how to assign the --anat_template argument, but I assume I will have to mount my SIGMA rat template and atlas folder.

Brad

[gdevenyi]

gabdesgreg/rabies:latest

This is not the correct container, should be ghcr.io/cobralab/rabies

[Gab-D-G]

Hi Brad,

You will need to relate the path from your atlas file to the container using the -v parameter, you can find details on this in the RABIES and docker documentation. Some like -v /home/rabies:/work_dir and then in you RABIES call --anat_template /work_dir/SIGMA_InVivo_Anatomical_Brain_template.nii.gz.

As @gdevenyi mentioned, I recommend you download ghcr.io/cobralab/rabies:latest instead, as you probably have an old RABIES version right now.

Gabriel

[hookeba]

Hello Gabriel!

Thank you for your hint. I specified the proper container, mounted my SIGMA rat template and atlas volume, and called --anat_template and --brain_mask:

docker run -it --rm --user $(id -u) -v $PWD/rabies:/rabies:ro -v $PWD/input_BIDS:/input_BIDS:ro -v $PWD/preprocess_outputs:/preprocess_outputs/ ghcr.io/cobralab/rabies:latest -p MultiProc preprocess /input_BIDS/ /preprocess_outputs/ --apply_STC --TR 1.0 --commonspace_reg masking=true,brain_extraction=false,template_registration=SyN,fast_commonspace=false --anat_template /rabies/SIGMA_InVivo_Anatomical_Brain_template.nii.gz --brain_mask /rabies/SIGMA_InVivo_Anatomical_Brain_mask.nii.gz --labels /rabies/SIGMA_InVivo_Anatomical_Brain_Atlas.nii.gz

I assume I should do the same for --WM_mask, --CSF_mask, and --labels as the defaults point to mouse (/home/rabies/.local/share/rabies/DSURQE_40micron*). Is it possible to omit the vascular mask?

Brad

[Gab-D-G]

You are right it will be necessary to similarly change the path for the mask files. If you are using version 0.5.5 (i.e. the latest), you will not need to specify anything onto the vascular_mask parameter, it is optional. Other you can just copy another brain mask and never use the vascular_mask for confound correction.