Preprocessing Rat Functional in vivo - GarzaLab/Documentation GitHub Wiki

Run RABIES from Docker

RABIES is very particular at the moment. I suggest you make a new folder for RABIES analysis and copy the raw data there.

The format for RABIES is here, check what you need. I suggest you delete the T1w 3D and just leave the T2w RARE. The func file needs to have run for example sub-9_ses-1_task-rest_run-1_bold.nii.gz. Same for the JSON.

As of now, we need to specify the atlas. For rats we are using the Fischer atlas now. For vascular, you need to specify something so just use the CSF mask for now and ignore that output later. Otherwise, it will run the mouse mask by default and possibly crash.

For the Anatomical image, I first run the preprocessing pipelines and copy the preprocessed image into the data/sub*/ses*/anat/ folder for better results.

Make sure the masks are binary or it will get stuck.

Example:

sudo docker run -it --rm -v /media/egarza/Elements2/projects/INB/GARZALAB/Pilotos/Prueba1/data:/nii_inputs:ro -v /media/egarza/Elements2/projects/INB/GARZALAB/Pilotos/Prueba1/derivatives/rabies:/outputs -v /home/egarza/atlases/Rat/Fischer344_nii_v3/Fischer344_nii_v3:/atlas gabdesgreg/rabies:latest /nii_inputs /outputs --tpattern seq --TR 2.1s --apply_despiking --disable_anat_preproc --anat_template /atlas/Fischer344_template.nii --brain_mask /atlas/Fischer344_mask.nii --WM_mask /atlas/Fischer344_TPM_WM_bin.nii.gz --CSF_mask /atlas/Fischer344_TPM_CSF_bin.nii.gz --vascular_mask /atlas/Fischer344_TPM_CSF_bin.nii.gz --labels /atlas/Fischer344_labels_v3.nii