1. Introduction to SPM Batching Guillaume Flandin Wellcome Trust Centre for Neuroimaging University College London MATLAB for Cognitive Neuroscience ICN, May 2008 from acquisition to publication…

2. Installing SPM using SVN  Install Subversion:  http://subversion.tigris.org/ http://subversion.tigris.org/  http://tortoisesvn.net/ http://tortoisesvn.net/ SPM repository your SPM working copy SPM Repository URLs: SPM5: svn://bread.fil.ion.ucl.ac.uk/spm/branches/spm5 SPM8: svn://bread.fil.ion.ucl.ac.uk/spm/trunk TBR: svn://bread.fil.ion.ucl.ac.uk/tools/TBR/trunk  Online instructions:  http://www.fil.ion.ucl.ac.uk/spm/local/svn/ http://www.fil.ion.ucl.ac.uk/spm/local/svn/  http://www.fil.ion.ucl.ac.uk/spm/local/tbr/ http://www.fil.ion.ucl.ac.uk/spm/local/tbr/ FIL & ICN only

3. TortoiseSVN: Checkout

4. TortoiseSVN: Update Case 1: your SPM files needed to be updated. Case 2: your SPM files are up-to-date.

5. MATLAB path Add Folder (and not with Subfolders) Remove older SPM versions from the path

6. Batching SPM{2,5,8}  SPM Extensions webpage: http://www.fil.ion.ucl.ac.uk/spm/ext/#batch_utils SPM99, SPM2 [1] http://en.wikibooks.org/wiki/SPM-Example_batch_script [2] http://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5http://en.wikibooks.org/wiki/SPM-Example_batch_scripthttp://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5  Call SPM functions directly [1,2] :  spm_realign  spm_slice_timing  spm_normalise  spm_write_sn  spm_smooth  spm_fmri_spm_ui  spm_spm  spm_FcUtil  spm_contrasts  Requires knowledge about input/output arguments of main SPM functions and about the SPM.mat structure. SPM8  Batch Editor:  “matlabbatch” structure.  Dependencies. SPM5  Job Manager:  “jobs” structure.  Virtual files.

7. SPM “jobs”  Goal: create a.mat file containing a Matlab structure ‘jobs’ similar to the one created using the GUI.  Tip: you only need to specify parameters that you would enter in the interface, the others will be automatically imported when executed.  The jobs structure will mimic the interface.  Batch mode:

8. Useful functions:  Select files: spm_select.m: [files,dirs] = spm_select(‘FPList',direc,filt) ex.: f = spm_select(‘FPList',‘C:\data\exp’,‘^fM.*\.img$’);  Job manager: spm_jobman.m: spm_jobman(‘run’,jobs); % execute a job spm_jobman(‘interactive’,jobs); % display a job in the GUI % jobs can also be a.mat filename  Overall structure of a batch script: spm(‘defaults’,‘fmri’); clear jobs % fill in jobs structure save(‘My_Batch.mat’,‘jobs’); spm_jobman(‘run’,jobs); See also:  fullfile  cellstr  kron  editfilenames*

9. Data organisation  Should be as generic as possible to ease batch script writing. Experiment subject1 structural functional session1 session2 … jobs stats model1 model2 … subject2 … scripts rfxmodel condition1 condition2 … Postscript (.ps) file: PDFCreator (http://www.pdfforge.org/)http://www.pdfforge.org/

10. A potention pipeline for preprocessing with SPM: RealignSegment Coregister Smooth Normalize: Write Raw functional images Update *.hdr mean.{img,hdr} rp_*.txt m*/c1*/c2*.{img,hdr} *_seg_sn.mat *_seg_inv_sn.mat Update *.hdr wm*. {img,hdr} sw*.{img,hdr} Anatomical image … Normalize: Write w*.{img,hdr} Group mean