My marsbar instructions

Marsbar instructions

Ikurniawan circa 2010

Creating homemade masks (create ‘rois’ folder in specific spm second level GLM, then save masks there clearly indicated):

• 1. From spm cluster:

     1. In spm: Results>choose contrast.

     2. In Marsbar: get spm cluster, choose contrast, ‘write ROI’ (on spm). Result is a cluster mask.

  2. Making a sphere:

• • 1. In spm: Results> choose contrast and note down a peak coordinate.

    2. In mArsbar: ROI definition> build>sphere> etc…

ROI analysis with anatomical AAL/ homemade/ cluster masks:

• 1. ROI definition> get spm cluster> choose spm.mat & relevant contrast

  2. Design> set design from file> choose spm.mat

  3. Data> extract ROI (default)>choose masks

  4. Data> export data> summary

  5. Data> export to> workspace

  6. Matlab var name: ‘rois’

  7. Result is a N x r x m matrix in matlab workspace. N= no of subjects, r = number of conditions/regressors, m= mask chosen in step c. E.g. size(rois)=76 X 4, 4 masks defined (caudate L & R, putamen L & R), 76=19 subjects x 4 experimental conditions (Lrew, HRew, LPun, HPun).

  8. On matlab: convert rois into N x r matrices for each mask (e.g. for x=1:8;roi(:,x)=rois(1+(x-1)*19:x*19);end for 8 conditions and 19 subejcts).

  9. Then copy roi matrix into excel, and run ANOVA on spss and create bar graphs.