Nia's Guild to SPM VBM

Information can be found on the SPM website (www.fil.ion.ucl.ac.uk/spm), look under ‘Documentation’ and find the Manual

NB All jobs are run by clicking the green ‘play’ button on top of the batch window

Make sure that the images are in the correct orientation. Images can be repositioned and reoriented using the ‘Display’ option in SPM

1. Start Matlab
2. If you have not done this already go to File → Set Path, then click on ‘Add with Subfolders’ and select the SPM code to add to the path
3. Type ‘spm fmri’ in the command window
4. Click on ‘Batch’ to open a new job window
5. Add in SPM → Spatial → Segment, this will segment the T1 image into grey matter and white matter

   Under ‘Data’ select all the T1 images

   N.B. If you have a lot of data you may have problems with memory so you may have to divide the images into two ‘Segment’ jobs or segment each image individually

6. Add in SPM → Tools → DARTEL Tools → Initial Import, produces roughly aligned grey and white matter images for the subjects, this takes about a minute per subject
7. Under ‘Parameter Files’ select all the ‘seg_sn’ files generated by the segmentation
8. Add in SPM → Tools → DARTEL Tools → Run DARTEL (create Template) to determine nonlinear deformations for warping the grey and white matter images so they match each other
   1. Click on ‘Images’ to get a new images ‘Images’ submenu, add in the ‘rc1’ files from the import
   2. Highlight the top ‘Images’ and click on ‘New Images’ in the bottom box, add in the ‘rc2’ files from the import in the same order as the ‘rc1’ files
9. Add in SPM → Tools → DARTEL Tools → Normalise to MNI Space to generate the smoothed warped grey matter images
   1. Under ‘DARTEL Template’ select ‘Template_6.nii’ from the previous step
   2. Change ‘Select according to’ to ‘Many subjects’ for VBM
   3. Under ‘Flow Fields’ add in the ‘u_rc1’ files generated by the previous step
   4. Under ‘Images’ add in two ‘Images’ subheadings
   5. In the first ‘Images’ add in the ‘c1’ files (from segmentation) in the same order as the flow fields
   6. In the second ‘Images’ add in the ‘c2’ files in the same order as the flow fields
   7. Under ‘Preserve’ change the option to ‘Preserve Amount’ for VBM
10. Add in SPM Add in SPM → Stats → Factorial design specification, specify the type of analysis you want to perform and submit the ‘smwc1’ files