Hi Bruce,
Thank you for your answer. What I forgot to mention is that I will not
be using FreeSurfer for the registration. We have our own registration
method that I prefer in this case.
I thought of using the -rl switch in mri_convert but as you mentioned
this will also resample the data. Do I understand correctly that it is
not possible to change the orientation in FreeSurfer without resampling?
Renske
Bruce Fischl wrote:
> Hi Renske,
>
> you can use the -rl mri/orig/001.mgz switch in mri_convert ("reslice
> like"). Note that depending on the resolution etc. of the 001.mgz it
> may do an additional interpolation. You shouldn't need to do this
> though for registration as it should read this information from the
> header. Martin Reuter (ccd) has some very nice tools for this kind of
> thing.
>
> cheers,
> Bruce
>
>
> On Tue, 18 Aug 2009, Renske de Boer wrote:
>
>> Hi,
>>
>> I would like to register a FreeSurfer segmentation (or actually the
>> corresponding T1 image) to another scan of the same subject. In order to
>> perform this registration, the mri/T1.mgz file needs to have the same
>> orientation as the original T1 scan (mri/orig/001.mgz). Resampling is
>> not necessary since I want to prevent multiple interpolations and
>> resampling is already necessary in the registration/transformation.
>>
>> How can I convert mri/T1.mgz to the same orientation as the original T1
>> scan?
>>
>> Thanks!
>> Renske
>>
>>
--
_____________________________________
Ms. Renske de Boer, MSc
Biomedical Imaging Group Rotterdam
Erasmus MC, University Medical Center
Rotterdam, the Netherlands
www.bigr.nl
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