SPM & SnPM instructions (with xjview and marsbar and bspmview)
IKurniawan - 2019
1. Run First level with SPM
2. Run second level with SnPM saving conXXXX+.fig and conXXXX-.fig files for + and – contrasts, and the corresponding SnPMT_image .img (containing both + and – results).
3. If needed, run second level analysis with a subject parametric modulator, using MultiSub: Simple Regression; 1 covariate of interest', (instead of the "MultiSub: One Sample T test on diffs/contrasts"); enter the subject regressor in "matlabbatch{1}.spm.tools.snpm.des.Corr.CovInt" (the "matlabbatch{1}.spm.tools.snpm.des.OneSampT.cov" is for cov of no interest.)
4. To run small volume correction, give the file path of the .nii mask as explicit mask, then (using the batch editor) change set cluster thresholding to 'none', and on inference batch: change type of thresholding as 'voxel'.
Viewing results:
- Type in xjview on matlab
- Go to the correct glm folder under Derivatives. Open conXXXX+.fig (double click) to get the list of supratreshold activity and then on xjview open (ctrl O) the corresponding .img file to explore the clusters.
- On xjview, choose only +, enter 3.26 at intensity (cluster forming threshold) and cluster size (written on .fig figure). The result should be identical to the glass brain on .fig image. Do the same for negative contrast, using the same img file but the -.fig
To create fxnal ROI mask:
- on xjview, go to the local maxima of the cluster, click 'pick cluster/info" and/or “select cluster”, File>save current image as mask (save in a folder called masks for later use).
- on marsbar, ROI definition>build>Image>(choose the img just created by xjview); this gives you the .mat equivalent of the .img
To extract subject by subject activity within an ROI:
- run second level SPM to get the equivalent SPM.mat of that contrast.
- proceed as usual (see mymarsbar instructions).
To get a list of anatomical locations
- Type bspmview on matlab (or using SPM GUI, toolbox>bspmview), open the .img file, change the intensity to 3.26. This list should be validated/corrected before publication.