To add to Jesper's comments--- I have ( a while ago ) gotten FNIRT to
work pretty well with mouse brains... basically one important trick
(as Jesper) pointed out was to not have your voxel dimensions be 0.2mm
(or whatever) but change it to 2mm.... also there was a bit of hacking
to change it so it doesn't use the MNI152_T1 brain as a reference...
at least for the fslvbm pipeline... just doing FNIRT itself I think
worked without too much difficulty...
dg
On Wed, Sep 8, 2010 at 4:31 AM, Jesper Andersson <[log in to unmask]> wrote:
> Dear Ekkehard,
>
> we have tried to write fnirt to be completely independent of scale/size of
> the brains. However I have personally never tested that properly (by running
> it e.g. on rats) so I think the "safest" way would be for you to simply
> scale all voxel-sizes by 10.
>
> There has been some questions about rat/mouse fnirting in the past so if you
> seek the archives you might find these postings and also mail addresses for
> people using it on rats/mice who you can ask for advice and their
> experiences.
>
> Good luck Jesper
>
> On 8 Sep 2010, at 09:05, Ekkehard Küstermann wrote:
>
>> Hi all,
>>
>> I'm trying to use FNIRT on rat and mice data.
>> Since the configuration files are apparently optimized for human/primate
>> sized brains I'm wondering whether somebody has any suggestions for
>> running FNIRT on such small volumes.
>> Or is the increase of the voxel size in the header the only alternative?
>>
>> Thanks for your help
>>
>> EKkehard
>>
>>
>> --
>> --------------------------------------------------------------------
>> Ekkehard Kuestermann, PhD (Dr.phil.II, Basel)
>>
>> Universitaet Bremen, MRS/MRI, ZKW
>> c/o FB2, AG Leibfritz
>> Leobener Strasse NW2/C
>> Postfach 33 04 40
>> D-28334 Bremen
>>
>> Tel: +49 (0)421 - 218 -63107 / -61930
>> Fax: +49 (0)421 - 218 -63102
>> Email: [log in to unmask]
>> --------------------------------------------------------------------
>>
>
--
David A Gutman, M.D. Ph.D.
Center for Comprehensive Informatics
Emory University School of Medicine
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