Hi Rebecca,
just one very general comment: if you look at John's 1997 paper on
spatial normalization, you can appreciate that every brain is enlarged
by a factor of about 1.4 or so when normalized to MNI space. This will
be slightly different when using DARTEL, but not by an order of
magnitude. Therefore, if you "preserve native-space resolution", you
already have to interpolate during spatial normalization as the volume
itself is enlarged. You may also want to consider that more voxels
substantially increase the number of statistical tests you perform
later-on, so it's a trade-off
Cheers,
Marko
Rebecca Lawson wrote:
> Hi Chris,
>
> Thanks for your reply. I've managed to create my dartel template in the
> native space of my high-res anatomical (by doing segment and then dartel
> import you can specify the voxel size of the dartel imported
> segmentation files). The issue is with then attempting to spatially
> normalise said high-res structurals and also functional images acquired
> at 1.5mm isotropic. I want to preserve these resolutions in the
> normalised images. I've gone down the 'combine deformations' route to
> normalisation with nice results, except that the normalised files
> (functional and structural) are written out at 2mm isotropic. Since each
> subjects flow field and the group Template6 are in correct native space,
> i guess it must be taking the resolution from the grey matter template
> (when working out sn.mat parameters from Template6 to the grey matter
> template) which is 2mm. Hence the thought about reslicing the grey
> matter template to the resolution I want my normalised images to be.
>
> Any further thoughts on how to get around this?
>
> Thanks again.
> B.
>
> On 17/08/2011 09:23, Christian Lambert wrote:
>> I guess you want to do a high resolution DARTEL in the native space of
>> your anatomicals? If so the up-sampling argument is not an issue. Try
>> this in matlab:
>>
>> edit spm_write_preproc8.m
>>
>> On line 211 change:
>> vx=1.5;
>>
>> For
>>
>> vx=0.75; %(or whatever your desired resolution is)
>>
>> And save. Now re-run spm New segment creating DATEL space
>> segmentations, and these will be in your desired resolution. You can
>> then re-run DARTEL to create your high resolution templates and warps.
>> Be warned, it is a lot slower (e.g. 60 subjects at 0.8mm took nearly a
>> week on a 12 core computer with 12Gb RAM)
>>
>> Hope that helps,
>>
>> - Chris
>>
>> P.S. Remember to change it back afterwards (easily overlooked in my
>> experience!)
>>
>> On Tue, Aug 16, 2011 at 5:11 PM, Rebecca Lawson
>> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>> Hello,
>>
>> I'd like to be able to reslice some of the spm template images to
>> higher resolutions (for example, to reslice the grey matter
>> template to .77x.77x.77mm). I have high resolution structural and
>> functional images and I am trying to improve normalisation using
>> dartel. I'd like some of the spm templates to match the resolution
>> of my images so that the resulting normalised images have their
>> resolutions preserved.
>>
>> Can anyone advise on how to reslice images to a different
>> isotropic resolution?
>>
>> Thanks in advance.
>>
>>
>
>
> --
> Dr Rebecca Lawson
> Cognitive Neuropsychiatry Group
> Institute of Cognitive Neuroscience
> University College London
> 17 Queen Square
> London
>
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn
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