Dear John and SPM expert,
I started working with SPM5b two months ago and have now some problems to
set the right defaults for segmentation. I hope you can help me.
I worked with the SPM GUI and set the following defaults. Now I want to
change to the segment.m. My question: Which defaults will I have to set to
get the same results like working with the SPM GUI:
OUTPUTFILES: Grey: native+modulated normalised
White: native+modulated normalised
CSF: native+modulated normalised
BIAS cor: save BIAS corrected
CUSTOM: TPM: C:\Matlab6p5\wgrey.nii;...\wwhite.nii\...wcsf.nii
GAUSSIAN: 2 2 2 4
AFFINE REG: Average sized template
WARPING REG: 1
WARP FR CUTOFF: 25
BIAS REG: 0.001
BIAS FWHM: 60mm
SAMP: 3
Working with the m-file, I set the following defaults, but the programm
gives me just the modulated images(mw...img) and the native segmented images
(c1*img,c2*img,c3*img) but I donīt get native+modulated normalised images
(mwc1w...img or mwc2w...img).
What did I forget to set?
Is it possible to get these to save them on disc?
The defaults I set in the m-file:
defaults.segment.estimate.priors = char(...
fullfile('C:\Matlab6p5\work','wgrey.nii'),...
fullfile('C:\Matlab6p5\work','wwhite.nii'),...
fullfile('C:\Matlab6p5\work','wcsf.nii'));
defaults.segment.estimate.reg = 0.001;
defaults.segment.estimate.cutoff = 25;
defaults.segment.estimate.samp = 3;
defaults.segment.estimate.bb = [[-78 78]' [-112 76]' [-50 85]'];
defaults.segment.estimate.affreg.smosrc = 8;
defaults.segment.estimate.affreg.regtype = 'mni';
defaults.segment.estimate.affreg.weight = '';
defaults.segment.write.cleanup = 1;
defaults.segment.write.wrt_cor = 1;
defaults.segment.write.wrt_brV = 1;
defaults.segment.graphics = 0;
disp('start segmentation');
range = [0 30];
P = spm_select(range,'image','Specify image(s) to be segmented');
end
V=spm_vol(P);
Q = defaults.segment.estimate.priors;
V = cat(1,V(:));
[VO, M] = spm_segment(V,Q,defaults.segment.estimate);
disp('segmentation done');
Please help me and tell which defaults I have to set or what I`ll have to
programme in the m-file to get the same results as working with the SPM GUI.
Thank you
Armin
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