Complementary questions: 

1) Glass brain is in Talairach space, right? 

2) Are results shown in MNI coordinates?

3) Is there a MNI version of glass brain?

Cheers

2016-03-28 17:24 GMT-03:00 Raphael F.C. <[log in to unmask]>:

Dear Guillaume,

When I do as you suggested in the last message, I get the following img:

And when I do it via the SPM gui I get the right one (below):

Do you happen to know what I am missing or what I did wrong?

I am using Windows 10, Matlab R2011a and SPM12 (6685)

Thanks in advance,

All the best,

Raphael

2015-01-21 10:20 GMT-02:00 Guillaume Flandin <[log in to unmask]>:

Dear Zhivago,

to save an image of the SPM glass brain non-interactively, you can run
the following in SPM12:

spm('defaults','fmri');
spm_get_defaults('cmdline',true)
spm_jobman('initcfg');

clear matlabbatch
matlabbatch{1}.spm.stats.results.spmmat = {'SPM.mat'};
matlabbatch{1}.spm.stats.results.conspec.contrasts = 1;
matlabbatch{1}.spm.stats.results.conspec.threshdesc = 'FWE';
matlabbatch{1}.spm.stats.results.conspec.thresh = 0.05;
matlabbatch{1}.spm.stats.results.conspec.extent = 0;
matlabbatch{1}.spm.stats.results.print = false;
spm_jobman('run',matlabbatch);

MIP = spm_mip(xSPM.Z,xSPM.XYZ,xSPM.M);

imwrite(MIP,gray(64),'MIP.png','png');

For your second question, have a look at spm_sections.m.

Best regards,
Guillaume.

On 21/01/15 11:55, Zhivago Kalathupiriyan wrote:
> What spm functions can be used to render a t-contrast and save the spm glass image?
>
> Also what are the spm functions that can be used to render a t-contrast on the sections of say, the mean functional image.
>
> Thanks,
> Zhivago...
>

--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG

--

Raphael F. Casseb

Medical Physicist, Ph.D. Student 

Medical Physics Lab - University of Campinas

Contact: +55 19 3521-8246

--

Raphael F. Casseb

Medical Physicist, Ph.D. Student 

Medical Physics Lab - University of Campinas

Contact: +55 19 3521-8246