The easiest way to create such scripts is via the Batch user
interface. You can save the batch file and modify the fields. The
various fields are related to each of the options on the user
interface, which also correspond to the sections in many of the
chapters of the manual.
Best regards,
-John
2011/7/14 Alejandro Cosa Liñán <[log in to unmask]>:
> Hello,
>
> Firstly, sorry for my English.
>
>
>
> I am trying to realign, coregister and normalize brains rat. I would like
> develop a script using spm_jobman command. When I create it, what are the
> struct fields needed for execute the script? For example:
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.template =
> {‘filetemplate’};
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.weight = '';
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.smosrc = 0;
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.smoref = 8;
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.regtype = 'mni';
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.cutoff = 20;
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.nits = 16;
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.reg = 1;
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.preserve = 0;
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.bb = [NaN NaN NaN;
> NaN NaN NaN];
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.vox = [2 2 2];
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.interp = 1;
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.wrap = [0 0 0];
>
> matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.prefix = 'w';
>
> spm_jobman(‘run’, matlabbatch);
>
>
>
> where can I find a tutorial that describes all the fields for realign,
> coregister and normalize and how does the script create?
>
> matlabbatch{1}.spm.spatial.normalise....,
> matlabbatch{1}.spm.spatial.coreg...., matlabbatch{1}.spm.spatial.realign....
>
>
>
> Thank you in advance
>
> Alex
>
>
