I think that this part is the cause of the problem:
> 7. the image to normalize is the subject's smoothed, modulated image (i
> didn't any errors in that either).
You seem to be trying to normalise the image twice over using the flow fields
(ie the flow fields have already been used to generate the the subject's
smoothed, modulated image).
I would also suggest trying the normalise to MNI space in the DARTEL toolbox
of SPM8.
Best regards,
-John
On Tuesday 05 May 2009 14:57, Devdutta W wrote:
> Hi John,
> I have examined the imported images, the template images as well as the
> images I want to normalize. All looked normal.
> Here is what I am doing:
>
> 1. I select the Normalize: Estimate module
> 2. select Template_6.nii for source image.
> 3. select grey.nii (from SPM) as template image.
> 4. all the rest of the options are as suggested int he manual.
> 5. For the Deformations module, I select the flow fields generated for
> that subject during the create template module.
> 6. The parameter file is the template_6_sn.mat.
> 7. the image to normalize is the subject's smoothed, modulated image (i
> didn't any errors in that either).
> 8. As before the other options are left as suggested in the manual.
>
> When I run the deformations module, once again all I get is a gray field.
> The evidence of underlying structure I mentioned last is very prominent.
>
> For the parameters file selection in the deformations module, I assume the
> template_6_sn.mat file is generated in the Normalize: Estimate module and
> that this is the one I should select.
>
> Can anybody shed some light on this?
>
> Regards,
> Devdutta
>
> On Fri, May 1, 2009 at 12:20 PM, John Ashburner
<[log in to unmask]>wrote:
> > > 1. Am I doing something wrong? If so, what could it be?
> >
> > I'm not sure what is happening here, but I would suggest you look at the
> > imported images, and template images (generated by DARTEL) for clues.
> >
> > > 2. Which files do I need to be selecting for the normalisation
> >
> > process?
> >
> > For the estimation of the warps, you would select the rc1 images and the
> > rc2
> > images (the "imported" images) as a seperate channels. For writing the
> > spatially normalised images, you would select the flow fields and the
> > images
> > that you want to spatially normalise.
> >
> > > 3. I read that for the normalisation to work it needs isotropic
> >
> > voxels.
> >
> > > Is this true? If so, our voxel size is -1.72 x 1.72 x 3. Can we
> >
> > apply
> >
> > > Dartel normalisation to this or do we have to re-size them to
> >
> > isotropic
> >
> > > size?
> >
> > The "imported" images are generated with isotropic voxel sizes.
> >
> > Best regards,
> > -John
> >
> > On Friday 01 May 2009 17:07, Devdutta W wrote:
> > > Hi,
> > > I have been trying to normalise the warped images to MNI space using
> > > Dartel. I am following the steps from "Using Dartel". I use the
> > > Normalise: estimate module then the Deformations module. When I view
> > > the normalised image, it is just gray field with evidence of some
> > > underlying structure. I am tempted to say it might just a flow-field
> > > or something similar it is displaying.
> > >
> > > Here are my questions:
> > >
> > > 1. Am I doing something wrong? If so, what could it be?
> > > 2. Which files do I need to be selecting for the normalisation
> >
> > process?
> >
> > > 3. I read that for the normalisation to work it needs isotropic
> >
> > voxels.
> >
> > > Is this true? If so, our voxel size is -1.72 x 1.72 x 3. Can we
> >
> > apply
> >
> > > Dartel normalisation to this or do we have to re-size them to
> >
> > isotropic
> >
> > > size?
> > >
> > > Any help in this matter will be greatly appreciated.
> > >
> > > Thank you,
> > > Devdutta
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