If you use the normalise to MNI space option (SPM8 version of DARTEL), then
you can set bounding boxes, voxel sizes etc. Note that I still need to
update the manual.
Best regards,
-John
On Wednesday 20 May 2009 17:07, Michael Erb wrote:
> Thanks Volkmar and John,
> that's the tool I need. I can use Composition with Deformation Field and
> Identity to select the different resolution of anatomical and functional
> images. But first I need to create a template image for each desired
> resolution. Is it possible to define the parameter (voxelsize, bounding
> box) like in normalise write? Or is it too difficult to include this
> option?
>
> Best regards,
> Michael.
>
> John Ashburner schrieb:
> > I would expect the DARTEL toolbox to do a better job than the
> > segmentation, especially given the option to "normalise to MNI space".
> > Note that there was a bug fix for the toolbox sent to the mailing list,
> > which will soon be included among the updates/fixes.
> >
> > As pointed out by Volkmar, the Deformations utility can be used to warp
> > whatever registered images you like in order to align them to MNI space.
> > Before using the segmentation/DARTEL, make sure that you have all your
> > within subject alignment finished (or that the coregistration uses the
> > anatomical scan as the reference image, one of your fMRI scans as the
> > source, and all the other fMRI - preferably realigned and resliced - as
> > other).
> >
> > Best regards,
> > -John
> >
> > On Tuesday 19 May 2009 19:51, Michael Erb wrote:
> >> Thank you John for the answer, but that is not my problem. I want to
> >> write the images (bias corrected anatomical and the functional) in the
> >> MNI space (warped). Is that possible with normalise write after creating
> >> a *_sn.mat file from the *_seg8.mat file using a script or is the DARTEL
> >> toolbox the right way to use the information (deformation field)?
> >>
> >> Best regards,
> >> Michael.
> >>
> >> John Ashburner schrieb:
> >>> There are a couple of slight bugs in the new segmentation user
> >>> interface, which will be ironed out in the next set of updates.
> >>> Currently, when you specify that the segmentation should write out a
> >>> bias corrected image, it writes out the bias field. If you request the
> >>> bias field, then it writes out the bias corrected image (note similar
> >>> behaviour when you request backward and forward spatial transform
> >>> files).
> >>>
> >>> If you have run the segmentation, and then want a bias corrected image,
> >>> then take a look at around line 112 of spm_preproc_run.m for clues
> >>> about how to do this.
> >>>
> >>> Best regards,
> >>> -John
> >>>
> >>> On Monday 18 May 2009 22:24, Michael Erb wrote:
> >>>> Hi John (or other well informed people),
> >>>> can you tell me how I can apply the normalisation parameter in
> >>>> *_seg8.mat to write the bias corrected anatomical and the functional
> >>>> images?
> >>>>
> >>>> Best regards,
> >>>> Michael.
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