Using SIGMA instead of Dsurge

[colon-perez]

Hello,
I want to use SIGMA because I have rat data. I started using it without specifying a template and it was not working see screenshot then I realized the atlas may be off. I want to use the SIGMA one using the command below

docker run -it --rm --platform linux/amd64 \
-v $PWD/Naive:/input_BIDS:ro \
-v $PWD/preprocess_outputs:/preprocess_outputs/ \
gabdesgreg/rabies:0.4.8 -p MultiProc preprocess /input_BIDS/ /preprocess_outputs/ --apply_STC --TR 4.0 --commonspace_reg masking=true,brain_extraction=false,template_registration=SyN,fast_commonspace=false --anat_robust_inho_cor apply=true,masking=false,brain_extraction=false,template_registration=SyN --anat_template=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Template.nii --brain_mask=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Mask.nii --WM_mask=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_WM_mask.nii --CSF_mask=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_CSF_mask.nii --vascular_mask=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Mask.nii --labels=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas/InVivo_Atlas/SIGMA_InVivo_Anatomical_Brain_Atlas.nii

But get this error

Traceback (most recent call last):
  File "/home/rabies/miniforge/bin/rabies", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/home/rabies/RABIES/scripts/rabies", line 3, in <module>
    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 178, in preprocess
    raise ValueError(f"--anat_template file {opts.anat_template} doesn't exists.")
ValueError: --anat_template file /Users/lmc0409/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Template.nii doesn't exists.

I want to stress the file does exits! I take the path and use it as is in fsleyes, and I can open the file.

[gdevenyi]

--anat_template=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Template.nii \
--brain_mask=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Mask.nii \
--WM_mask=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_WM_mask.nii \
--CSF_mask=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_CSF_mask.nii \
--vascular_mask=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Mask.nii \
--labels=/Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas/InVivo_Atlas/SIGMA_InVivo_Anatomical_Brain_Atlas.nii

You need to provide the atlas files at a path mounted into the container. You are giving a path on the host system which the container cannot access.

[Gab-D-G]

In your case, you could add -v /Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1:/atlas_folder to gain access to the atlas files, and the command may look like this:

docker run -it --rm --platform linux/amd64 \
-v $PWD/Naive:/input_BIDS:ro \
-v $PWD/preprocess_outputs:/preprocess_outputs/ \
-v /Users/luis/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1:/atlas_folder \
gabdesgreg/rabies:0.4.8 -p MultiProc preprocess /input_BIDS/ /preprocess_outputs/ --apply_STC --TR 4.0 --commonspace_reg masking=true,brain_extraction=false,template_registration=SyN,fast_commonspace=false --anat_robust_inho_cor apply=true,masking=false,brain_extraction=false,template_registration=SyN --anat_template=/atlas_folder/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Template.nii --brain_mask=/atlas_folder/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Mask.nii --WM_mask=/atlas_folder/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_WM_mask.nii --CSF_mask=/atlas_folder/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_CSF_mask.nii --vascular_mask=/atlas_folder/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Mask.nii --labels=/atlas_folder/SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas/InVivo_Atlas/SIGMA_InVivo_Anatomical_Brain_Atlas.nii