ln CSPM, click the ‘Preclinical’ button
In the ‘Setup’ tab, make sure ‘Rat’ is selected (with a scale factor of 8), paste your ‘projects’ folder path into the ‘Project folder’ box and the folder path of your ‘stats' folder into the ‘Stats’ box. In the boxes under 'Rat (unscaled)’, paste in the folder path for the unscaled SIGMA rat brain template, GM, WM and CSF.
In the ‘Main’ tab, you should now see all of your subject folder names in the left hand panel.
Tick the ‘DTI’, ‘fMRI' and ‘T2map’ boxes and click the ‘Preprocess to Coreg’ button. This will create ‘coreg’ folders in each subject’s ‘DTI’, ‘fMRI’ and ‘T2map' folders, with the relevant file in each folder, and a text document file named 'coreg_not_done’.
Go into as detailed in steps 10-12 of the confluence page ‘File/Folder Setup and Preparation for Preprocessing’.
once you run the ‘Preprocess to Coreg’ steps 10-12, it will create ‘coreg’ folders in each of these folders