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’.
Realign i.e. coregister the DTI and fMRI images in the ‘coreg’ folders, for each subject, as detailed in steps 10-12 of the confluence page ‘File/Folder Setup and Preparation for Preprocessing’. Write down the pitch, roll, yaw and crosshair position values in the the text document file named ‘coreg_not done’ and rename this file to ‘coreg_*date*'. There is no need to do this for the ‘T2map’ files as they were realgined i.e. coregistered in steps 9-14 from the confluence page ‘File/Folder Setup and Preparation for Preprocessing’.
Now, go back to the ‘Preclinical’ GUI and unselect the ‘T2map’ box and select the ‘VBM’ box i.e. make sure ‘DTI’, ‘fMRI’ and ‘VBM’ boxes are ticked and that the ‘T2map’ box is unticked.
Then click into the ‘DTI’ (doesn’t exist but it will soon), ‘fMRI’ and ‘VBM’ tabs and set the parameters you desire. E.g.
If you are unsure what value to enter in the ‘Normalised voxel size’ box, open one of your raw T2map images in MRIcron, click ‘Window’ → ‘Information’ and look at the values in the ‘Spacing’ column.
Click the ‘Preprocess after Coreg’ button. This step will take a few hours to complete, depending on how many subjects you have.
Once the ‘Preprocess after Coreg’ step is finished, all of the files necessary for analysis will be in your ‘stats’ folder.
NOTE: For step 6: CHECK WITH PAUL that it is possible to run VBM, DTI and fMRI ‘preprocess after coreg’ all at the same time (once its working for DTI, I think it will be possible to run all at the same time).