Hi,
Here's a script I wrote that will do a 6 DOF alignment of the AC-PC, based on a 12 DOF alignment to the standard template. So just take your 12 DOF FLIRT transformation and run it through this to get what you want. It's pretty self explanatory.
All the best,
Mark
On 28 Aug 2012, at 00:47, Kai Schlamp <[log in to unmask]> wrote:
> Hi Christine,
>
> then I should better say ... without changing the matrix size or voxel size.
>
> On Mon, 27 Aug 2012 23:34:30 +0000, Christine Zakrzewski <[log in to unmask]> wrote:
>
>>
>> just a quick fyi--deobliquing your data interpolates/resamples it.good luck.christine
>>> Date: Tue, 28 Aug 2012 00:10:57 +0100
>>> From: [log in to unmask]
>>> Subject: [FSL] deoblique volume and prealign to ac-pc
>>> To: [log in to unmask]
>>>
>>> Hello FSLers,
>>>
>>> for some special reasons (like manually creating masks) I'd like my original volumes to be deobliqued and prealigned to ac-pc (without being resampled or scaled, just rotated). I look for doing this somehow automatically.
>>> So I tried to register (flirt with 12 dof) my volumes to a MNI standard template, get just the transformation matrix, extract only the rotation and translation part (using avscale), set the translation there to 0 (last column) and applied that new matrix (rotation only) to the original image (by using itself as reference in flirt). Unfortunately the center of the brain volume still moves away from the center of the whole volume.
>>> Does someone have a better idea how to accomplish this?
>>>
>>> Best regards,
>>> Kai
>>
>
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