Set up a batch job via the user interface. If you click the Save button, then
you can give it a name with a .m extension. This will tell you how the
existing job was set up. Once a job is set up, then the stuff in the "jobs"
variable can be run by:
spm_jobman('run',jobs)
Best regards,
-John
On Wednesday 11 June 2008 09:10, you wrote:
> Many thanks John.
> In fact, I also have a side-question regarding programming SPM. I would
> prefer to use m file to control SPM rather than pushing buttons especially
> when I have tones of images. E.g. how could I use m file to control SPM for
> spatial normalization? Both write & estimate + write only.
>
> Many thanks indeed,
> Edward
>
> On Fri, Jun 6, 2008 at 02:22, John Ashburner <[log in to unmask]> wrote:
> > > So are you saying DARTEL might work if I could somehow segment my FA
> > > maps into WM and GM images (e.g. in analyze format)?
> >
> > That's the case at the moment.
> >
> > > If you don't mind, could you be more specific about what sort of extra
> > > coding I need to program to get DARTEL work on animal brain? Or are
> > > there any way to "make up" my images, .e.g. deliberately scale up the
> > > images or change manually the voxel size in the header to match that of
> > > human
> >
> > brain?
> >
> > If you can scale them up by the right amount, then that may do the trick.
> > Alternatively, various adjustments to the regularisation (and smoothing)
> > settings may help.
> >
> > Best regards,
> > -John
> >
> > > On Thu, Jun 5, 2008 at 7:12 PM, John Ashburner <[log in to unmask]>
> > >
> > > wrote:
> > > > This isn't going to work. DARTEL works with segmented images, so if
> >
> > you
> >
> > > > had
> > > > images of GM and WM, then you may have a better chance. Also the
> > > > settings are such that smoothing etc is all set up for human-sized
> > > > brains. To work with other types of brains, you'll need to do (or
> > > > have someone else do) a bit
> > > > more extra coding.
> > > >
> > > > Best regards,
> > > > -John
> > > >
> > > > On Thursday 05 June 2008 08:35, Edward Hui wrote:
> > > > > Hi Everyone,
> > > > >
> > > > > I should also mention that I do not have any priors. I also do not
> >
> > have
> >
> > > > > a template space defined.
> > > > >
> > > > > Before I push button for DARTEL, I have series of affined
> > > > > transformed FA map of 5 rats. Then I wanted to put all these
> > > > > registered/warped FA maps into DARTEL to generate a FA rat
> > > > > template.
> > > > >
> > > > > However, it did not seem to work as I mentioned before where I have
> > > >
> > > > really
> > > >
> > > > > blurry generated templates.
> > > > >
> > > > > Any help would be appreciated again and thank you.
> > > > >
> > > > > Edward
|