Hello everyone,
I've been using code that has worked under SPM2 and SPM5 to go back
and forth between coordinates in an individual subject's MRI space to
MNI space, inspired by John's Gems 5 and 11:
http://www.sph.umich.edu/~nichols/JohnsGems2.html#Gem5
However, the procedure seems to need updating for SPM8 (and/or perhaps
for the Nifti format). Just thought I'd share what I've come up with.
Note: the following jobman runs can be done entirely in the GUI, but
as I'm using the normalization routines outside the standard SPM
processing stream, I wanted to generate command-line equivalents.
These have changed since previous versions of SPM as well.
To generate the Deformation file (y_Blah.nii), as spm_sn2def.m no
longer exists, I do the following -- many thanks to Guillaume for
getting me started:
matlabbatch{1}.spm.util.defs.comp{1}.sn2def.matname = {'Blah_sn.mat'};
matlabbatch{1}.spm.util.defs.comp{1}.sn2def.vox = NaN(1,3);
matlabbatch{1}.spm.util.defs.comp{1}.sn2def.bb = NaN(2,3);
matlabbatch{1}.spm.util.defs.ofname = 'Blah';
matlabbatch{1}.spm.util.defs.fnames = '';
matlabbatch{1}.spm.util.defs.interp = 1;
spm_jobman('run',matlabbatch);
Then to create the inverse deformation (what would have been called
iy_Blah.img in SPM2/SPM5):
matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.sn2def.matname =
{'Blah_sn.mat'};
matlabbatch{1}.spm.util.defs.comp{1}.sn2def.vox = NaN(1,3);
matlabbatch{1}.spm.util.defs.comp{1}.sn2def.bb = NaN(2,3);
matlabbatch{1}.spm.util.defs.comp{1}.inv.space = {'wBlah.nii,1'};
matlabbatch{1}.spm.util.defs.ofname = 'iBlah';
matlabbatch{1}.spm.util.defs.fnames = '';
matlabbatch{1}.spm.util.defs.interp = 1;
spm_jobman('run',matlabbatch);
This creates y_iBlah.nii... but for some reason, this volume has
dimensions [81 98 83 1 3] (i.e., the 3 deformation fields are now
defined in the fifth dimension rather than fourth). So John's Gem #5
needs to be modified with the following simple change:
P = [repmat(P,3,1) [',1,1';',1,2';',1,3']];
Cheers,
Sarang
--
Sarang S. Dalal, Ph.D.
INSERM U821-Dynamique Cérébrale et Cognition
http://tempest.ucsf.edu/~sarang/
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tel: +33 4 72 13 89 15
fax: +33 4 72 13 89 01
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