Dear John,
Thanks for your input. It was that mail that prompted my questions, in
a manner of speaking. I think I'll go for DARTEL based on this and the
Klein et al article. One thing, though: You say that the registration
should take 20 minutes. However, I spent some 2 hours watching the
normalization step do it's magic yesterday. Is there perhaps some
problem with my setup or hardware that's causing the slowing?
On a tangential note, for the list: Does anyone know of a "recepie"
for using DARTEL normalization on fMRI data? The Dartel guide is
somewhat sparse when it comes to that subject (at least for those of us
that are rather new to the game), and I haven't been able to find
anything through Google, either.
Thanks!
Haakon
John Ashburner skrev:
> The actual registration takes about 20 minutes per subject, which could be run
> overnight. I would suggest using the version in SPM8 (see email from
> yesterday), which has the option to create DARTEL aligned images in MNI
> space.
>
> One of the problems with methods that are able to achieve more extreme
> deformations is that some regions can shrink by a great deal, and this
> results in signal loss from those regions - especially after smoothing. The
> option that warps to MNI space attempts to prevent the loss of this fMRI
> signal by (hopefully) generating smoothed spatially normalised images in a
> slightly more optimal way.
>
> Best regards,
> -John
>
>
> On Thursday 30 April 2009 16:40, Haakon Engen wrote:
>
>> Dear fellow SPM'ers,
>>
>> I am currently setting up a preprocessing pipeline for a group of 40
>> subjects.Normalization is rather important for this project, seeing as
>> how I am planning to do DCM modeling on rather small subcortical ROI's.
>> I am therefore considering using DARTEL to spatially normalize my fMRI
>> volumes. My initial test runs have been successful, but it has dawned on
>> me that DARTEL normalization takes quite a bit longer than standard
>> normalization.
>>
>> I was therefore wondering if any of you have experience with DARTEL
>> normalization and could inform whether or not it is worth the extra
>> processing time, with regards to accuracy
>>
>> Second I have some questions regarding the precise procedure of doing
>> DARTEL with regard to fMRI normalization. Is it necessary to calculate
>> the Templates and flow fields for each subject, or should I include all
>> the GM and WM segmented images for all subjects in one calculation?
>>
>> Thanks in advance,
>> Haakon Engen
>> Graduate student/Research Assistant
>> University of Oslo, Norway
>>
>
>
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