Dear SPM-experts,
we conducted a fMRI study and are experiencing very strange effects during the "realign & unwarp"-step of preprocessing using SPM 8.
During the first step of preprocessing we calculated the phase map for each subject. Upon visual examination using SPM and MRIcron, the phase map looked like we would have expected it to look.
However, when we used the phase map file during the next of preprocessing, realign and unwarp, the effect of the phasemap seems to be somewhat inverted.
We expected the unwarped brain to become somewhat bigger, as positive values of the phase map in the frontal lobe should result in this part of the image getting stretched. Instead, the frontal parts of the images decreased in size (see attachment "PhaseMapPositive.jpg").
In an analogous manner, the parts of the brain corresponding to negative values in the phasemap, which we would have expected to shrink, expanded upon unwarping (see attachment "PhaseMapNegative.jpg").
The effect occurs with all subjects of the study, although the extend of the effect seems to differ slightly. We also tried to do the preprocessing on different computers running different versions of SPM8 but did get identical results. Attached you will also find batch used to do the preprocessing, so that you may check for any erroneous parameters ("Preprocessing_job010.m").
We don't currently know what causes this effect and would be very grateful for any input.
Best regards and many thanks for taking time to help with our problem,
Max Hilger
%-----------------------------------------------------------------------
% Job configuration created by cfg_util (rev $Rev: 4252 $)
%-----------------------------------------------------------------------
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.phase = {'T:\Data_NifTi\0166KF-010-01LK_001_003_gre_field_mapping_mag_phas.nii,1'};
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.magnitude = {'T:\Data_NifTi\0166KF-010-01LK_001_002_gre_field_mapping_mag_phas.nii,1'};
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.et = [10 14.76];
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.maskbrain = 0;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.blipdir = 1;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.tert = 40.96;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.epifm = 0;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.ajm = 0;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.uflags.method = 'Mark3D';
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.uflags.fwhm = 10;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.uflags.pad = 0;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.uflags.ws = 1;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.mflags.template = {'C:\Program Files\MATLAB\R2008b\spm8\templates\T1.nii'};
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.mflags.fwhm = 5;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.mflags.nerode = 2;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.mflags.ndilate = 4;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.mflags.thresh = 0.5;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.defaults.defaultsval.mflags.reg = 0.02;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.session.epi = {'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,1'};
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.matchvdm = 0;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.sessname = 'session';
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.writeunwarped = 0;
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.anat = '';
matlabbatch{1}.spm.tools.fieldmap.presubphasemag.subj.matchanat = 0;
%%
matlabbatch{2}.spm.spatial.realignunwarp.data.scans = {
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'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,604'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,605'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,606'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,607'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,608'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,609'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,610'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,611'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,612'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,613'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,614'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,615'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,616'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,617'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,618'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,619'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,620'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,621'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,622'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,623'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,624'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,625'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,626'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,627'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,628'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,629'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,630'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,631'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,632'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,633'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,634'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,635'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,636'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,637'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,638'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,639'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,640'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,641'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,642'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,643'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,644'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,645'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,646'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,647'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,648'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,649'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,650'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,651'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,652'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,653'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,654'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,655'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,656'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,657'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,658'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,659'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,660'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,661'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,662'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,663'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,664'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,665'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,666'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,667'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,668'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,669'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,670'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,671'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,672'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,673'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,674'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,675'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,676'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,677'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,678'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,679'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,680'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,681'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,682'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,683'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,684'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,685'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,686'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,687'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,688'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,689'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,690'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,691'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,692'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,693'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,694'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,695'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,696'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,697'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,698'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,699'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,700'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,701'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,702'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,703'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,704'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,705'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,706'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,707'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,708'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,709'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,710'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,711'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,712'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,713'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,714'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,715'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,716'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,717'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,718'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,719'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,720'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,721'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,722'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,723'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,724'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,725'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,726'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,727'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,728'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,729'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,730'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,731'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,732'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,733'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,734'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,735'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,736'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,737'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,738'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,739'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,740'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,741'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,742'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,743'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,744'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,745'
'T:\Data_NifTi\0166KF-010-01LK_001_004_ep2d_mosaic.nii,746'
};
%%
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1) = cfg_dep;
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1).tname = 'Phase map (vdm* file)';
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1).tgt_spec{1}(1).value = 'image';
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1).tgt_spec{1}(2).value = 'e';
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1).sname = 'Presubtracted Phase and Magnitude Data: Voxel displacement map (Subj 1, Session 1)';
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan(1).src_output = substruct('()',{1}, '.','vdmfile', '{}',{1});
matlabbatch{2}.spm.spatial.realignunwarp.eoptions.quality = 1;
matlabbatch{2}.spm.spatial.realignunwarp.eoptions.sep = 4;
matlabbatch{2}.spm.spatial.realignunwarp.eoptions.fwhm = 5;
matlabbatch{2}.spm.spatial.realignunwarp.eoptions.rtm = 0;
matlabbatch{2}.spm.spatial.realignunwarp.eoptions.einterp = 7;
matlabbatch{2}.spm.spatial.realignunwarp.eoptions.ewrap = [0 0 0];
matlabbatch{2}.spm.spatial.realignunwarp.eoptions.weight = '';
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.basfcn = [12 12];
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.regorder = 1;
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.lambda = 100000;
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.jm = 0;
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.fot = [4 5];
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.sot = [];
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.uwfwhm = 4;
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.rem = 1;
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.noi = 5;
matlabbatch{2}.spm.spatial.realignunwarp.uweoptions.expround = 'Average';
matlabbatch{2}.spm.spatial.realignunwarp.uwroptions.uwwhich = [2 1];
matlabbatch{2}.spm.spatial.realignunwarp.uwroptions.rinterp = 7;
matlabbatch{2}.spm.spatial.realignunwarp.uwroptions.wrap = [0 0 0];
matlabbatch{2}.spm.spatial.realignunwarp.uwroptions.mask = 1;
matlabbatch{2}.spm.spatial.realignunwarp.uwroptions.prefix = 'u';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1) = cfg_dep;
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1).tname = 'Reference Image';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1).tgt_spec{1}(1).value = 'image';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1).tgt_spec{1}(2).value = 'e';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1).sname = 'Realign & Unwarp: Unwarped Mean Image';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1).src_output = substruct('.','meanuwr');
matlabbatch{3}.spm.spatial.coreg.estimate.source = {'T:\Data_NifTi\0166KF-010-01LK_001_005_t1_mpr_ns_sag.nii,1'};
matlabbatch{3}.spm.spatial.coreg.estimate.other = {''};
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
matlabbatch{4}.spm.spatial.preproc.data(1) = cfg_dep;
matlabbatch{4}.spm.spatial.preproc.data(1).tname = 'Data';
matlabbatch{4}.spm.spatial.preproc.data(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{4}.spm.spatial.preproc.data(1).tgt_spec{1}(1).value = 'image';
matlabbatch{4}.spm.spatial.preproc.data(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{4}.spm.spatial.preproc.data(1).tgt_spec{1}(2).value = 'e';
matlabbatch{4}.spm.spatial.preproc.data(1).sname = 'Coregister: Estimate: Coregistered Images';
matlabbatch{4}.spm.spatial.preproc.data(1).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{4}.spm.spatial.preproc.data(1).src_output = substruct('.','cfiles');
matlabbatch{4}.spm.spatial.preproc.output.GM = [0 0 1];
matlabbatch{4}.spm.spatial.preproc.output.WM = [0 0 1];
matlabbatch{4}.spm.spatial.preproc.output.CSF = [0 0 0];
matlabbatch{4}.spm.spatial.preproc.output.biascor = 1;
matlabbatch{4}.spm.spatial.preproc.output.cleanup = 0;
matlabbatch{4}.spm.spatial.preproc.opts.tpm = {
'C:\MatlabScripts\spm\spm8_old\spm8\tpm\grey.nii'
'C:\MatlabScripts\spm\spm8_old\spm8\tpm\white.nii'
'C:\MatlabScripts\spm\spm8_old\spm8\tpm\csf.nii'
};
matlabbatch{4}.spm.spatial.preproc.opts.ngaus = [2
2
2
4];
matlabbatch{4}.spm.spatial.preproc.opts.regtype = 'mni';
matlabbatch{4}.spm.spatial.preproc.opts.warpreg = 1;
matlabbatch{4}.spm.spatial.preproc.opts.warpco = 25;
matlabbatch{4}.spm.spatial.preproc.opts.biasreg = 0.0001;
matlabbatch{4}.spm.spatial.preproc.opts.biasfwhm = 60;
matlabbatch{4}.spm.spatial.preproc.opts.samp = 3;
matlabbatch{4}.spm.spatial.preproc.opts.msk = {''};
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1) = cfg_dep;
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1).tname = 'Parameter File';
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1).tgt_spec{1}(1).value = 'mat';
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1).tgt_spec{1}(2).value = 'e';
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1).sname = 'Segment: Norm Params Subj->MNI';
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1).src_exbranch = substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{5}.spm.spatial.normalise.write.subj.matname(1).src_output = substruct('()',{1}, '.','snfile', '()',{':'});
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep;
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1).tname = 'Images to Write';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1).tgt_spec{1}(1).value = 'image';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1).tgt_spec{1}(2).value = 'e';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1).sname = 'Realign & Unwarp: Unwarped Images (Sess 1)';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1).src_output = substruct('.','sess', '()',{1}, '.','uwrfiles');
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2) = cfg_dep;
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2).tname = 'Images to Write';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2).tgt_spec{1}(1).name = 'filter';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2).tgt_spec{1}(1).value = 'image';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2).tgt_spec{1}(2).name = 'strtype';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2).tgt_spec{1}(2).value = 'e';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2).sname = 'Coregister: Estimate: Coregistered Images';
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2).src_exbranch = substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(2).src_output = substruct('.','cfiles');
matlabbatch{5}.spm.spatial.normalise.write.roptions.preserve = 0;
matlabbatch{5}.spm.spatial.normalise.write.roptions.bb = [-78 -112 -50
78 76 85];
matlabbatch{5}.spm.spatial.normalise.write.roptions.vox = [3 3 3];
matlabbatch{5}.spm.spatial.normalise.write.roptions.interp = 1;
matlabbatch{5}.spm.spatial.normalise.write.roptions.wrap = [0 0 0];
matlabbatch{5}.spm.spatial.normalise.write.roptions.prefix = 'w';
matlabbatch{6}.spm.spatial.smooth.data(1) = cfg_dep;
matlabbatch{6}.spm.spatial.smooth.data(1).tname = 'Images to Smooth';
matlabbatch{6}.spm.spatial.smooth.data(1).tgt_spec{1}(1).name = 'filter';
matlabbatch{6}.spm.spatial.smooth.data(1).tgt_spec{1}(1).value = 'image';
matlabbatch{6}.spm.spatial.smooth.data(1).tgt_spec{1}(2).name = 'strtype';
matlabbatch{6}.spm.spatial.smooth.data(1).tgt_spec{1}(2).value = 'e';
matlabbatch{6}.spm.spatial.smooth.data(1).sname = 'Normalise: Write: Normalised Images (Subj 1)';
matlabbatch{6}.spm.spatial.smooth.data(1).src_exbranch = substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
matlabbatch{6}.spm.spatial.smooth.data(1).src_output = substruct('()',{1}, '.','files');
matlabbatch{6}.spm.spatial.smooth.fwhm = [9 9 9];
matlabbatch{6}.spm.spatial.smooth.dtype = 0;
matlabbatch{6}.spm.spatial.smooth.im = 0;
matlabbatch{6}.spm.spatial.smooth.prefix = 's';
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