you can change the orientation without reslicing, but if the voxel
dimensions of the 001.mgz are different from the orig.mgz then it will
have to reslice. I don't see why you need to at all though - both contain
ras2vox xforms that tell you how to initialize a transform.
cheers
Bruce
On Tue, 18 Aug 2009, Renske de Boer wrote:
> 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
>>>
>>>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
