SurfRend SPM Toolbox

This toolbox allows you to display fMRI activation maps from FSL's FEAT, or other SPM volumes, on Freesurfer cortical surface models for visualization.

Download and install instructions: http://spmsurfrend.sourceforge.net

PAL All-Rest

Notes

  • SPM must be installed and added to the MATLAB path.
  • SurfRend must be added to the SPM toolbox folder.
  • The FS_spm_CanonicalBrain subject must be added to the Freesurfer subjects area.
  • The Freesurfer matlab directory must be added to the MATLAB path.
  • The “canonical brain” is the Colin27 single subject average brain in MNI152 space.
    • a.k.a. single_subj_T1 in the SPM canonical folder.

Processing

  1. Downsample stat map into MNI152 2mm space if needed.
    ID.mat = 
    1 0 0 0
    0 1 0 0
    0 0 1 0
    0 0 0 1
    flirt -in stat_map.nii.gz -ref /usr/local/fsl/data/standard/avg152T1.nii.gz -out stat_map_2mm -init ../ID.mat -applyisoxfm 2
  2. Switch to ANALYZE filetype.
    fslchfiletype ANALYZE stat_map_2mm.nii.gz
  3. Follow the authors' instructions in the SurfRend Tutorial. pdf
    1. Make sure to choose some sort of >0 threshold, even in binarized/pre-thresholded volumes, or surfrend will process every voxel and take a very long time.
    2. Processing time depends on the number of suprathreshold voxels, so I find it useful to do a quick orientation test (to check to make sure the blobs on the surface match the blobs in my volume) with a very high threshold first.
  4. Display results in NeuroLens.
    1. We have also tried 3D Slicer, but it seems to only take label overlays (i.e. not the continuous-valued overlays of SurfRend).
neuroimaging/surfrend.txt · Last modified: 2011/01/05 9:19 am PST by John Colby
 
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