bump version, merge pull request #16 from AMYPAD/centiloid

spm12/coreg_spm_m.m → spm12/amypad_coreg.m

@@ -1,4 +1,4 @@
-function [M, x] = coreg_spm_m(imref, imflo, costfun, sep, tol, fwhm, params, graphics, visual)
+function [M, x] = amypad_coreg(imref, imflo, costfun, sep, tol, fwhm, params, graphics, visual)
     if visual>0
         Fgraph = spm_figure('GetWin','Graphics');
         Finter = spm_figure('GetWin','Interactive');

spm12/amypad_coreg_modify_affine.m

@@ -0,0 +1,7 @@
+function out = amypad_coreg_modify_affine(imflo, M)
+    VF = strcat(imflo,',1');
+    MM = zeros(4,4);
+    MM(:,:) = spm_get_space(VF);
+    spm_get_space(VF, M\MM(:,:));
+    out = 0;
+end

spm12/amypad_normw.m

@@ -0,0 +1,10 @@
+function out = amypad_normw(def_file, flist4norm)
+    job.subj.def = {def_file};
+    job.subj.resample = flist4norm;
+    job.woptions.bb = [NaN, NaN, NaN; NaN, NaN, NaN];
+    job.woptions.vox = [2, 2, 2];
+    job.woptions.interp = 4;
+    job.woptions.prefix = 'w';
+    spm_run_norm(job);
+    out=0;
+end

spm12/resample_spm_m.m → spm12/amypad_resample.m

@@ -1,4 +1,4 @@
-function out = resample_spm_m(imref, imflo, M, f_mask, f_mean, f_interp, f_which, f_prefix)
+function out = amypad_resample(imref, imflo, M, f_mask, f_mean, f_interp, f_which, f_prefix)
     %-Reslicing parameters
     rflags.mask = f_mask;
     rflags.mean = f_mean;

spm12/amypad_seg.m

@@ -0,0 +1,46 @@
+function [param,invdef,fordef] = amypad_seg(f_mri, spm_path, nat_gm, nat_wm, nat_csf, store_fwd, store_inv, visual)
+    job.channel.vols = {strcat(f_mri,',1')};
+    job.channel.biasreg = 0.001;
+    job.channel.biasfwhm = 60;
+    job.channel.write = [0, 0];
+    job.tissue(1).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,1']};
+    job.tissue(1).ngaus = 1;
+    job.tissue(1).native = [nat_gm, 0];
+    job.tissue(1).warped = [0, 0];
+    job.tissue(2).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,2']};
+    job.tissue(2).ngaus = 1;
+    job.tissue(2).native = [nat_wm, 0];
+    job.tissue(2).warped = [0, 0];
+    job.tissue(3).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,3']};
+    job.tissue(3).ngaus = 2;
+    job.tissue(3).native = [nat_csf, 0];
+    job.tissue(3).warped = [0, 0];
+    job.tissue(4).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,4']};
+    job.tissue(4).ngaus = 3;
+    job.tissue(4).native = [0, 0];
+    job.tissue(4).warped = [0, 0];
+    job.tissue(5).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,5']};
+    job.tissue(5).ngaus = 4;
+    job.tissue(5).native = [0, 0];
+    job.tissue(5).warped = [0, 0];
+    job.tissue(6).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,6']};
+    job.tissue(6).ngaus = 2;
+    job.tissue(6).native = [0, 0];
+    job.tissue(6).warped = [0, 0];
+    job.warp.mrf = 1;
+    job.warp.cleanup = 1;
+    job.warp.reg = [0, 0.001, 0.5, 0.05, 0.2];
+    job.warp.affreg = 'mni';
+    job.warp.fwhm = 0;
+    job.warp.samp = 3;
+    job.warp.write = [store_fwd, store_inv];
+    if visual>0
+        Finter = spm_figure('GetWin','Interactive');
+    end
+    spm_jobman('initcfg');
+    segout = spm_preproc_run(job);
+    param  = segout.param{1};
+    invdef = segout.invdef{1};
+    fordef = segout.fordef{1};
+    %disp(segout);
+end