Hi,
In the last step you can choose your output FOV and resolution. The easiest way to have full control over that is to use the ApplyXFM GUI, but it is also fairly easy to achieve in the command line. The 12 DOF transformation to MNI is used to determine where the AC, PC and mid-plane are in your brain image but are not used to determine any of the output resolution or FOV in the last step.
All the best,
Mark
> On 25 Aug 2017, at 16:24, Alexandre Boutet <[log in to unmask]> wrote:
>
> Thank you Mark.
>
> The issue is I do want to keep my T1s unchanged in dimension. Will these steps change my original image volume? If I use 12 DOF I will change volumes in my T1 won't I?
>
> Sorry, just to clarify all this is doing is aligning my scans with 6 parameters only.
>
>
> Sent from my iPhone
>
>
>> On Aug 25, 2017, at 11:16, Mark Jenkinson <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> You can do this with these steps (most of them beneficial for later analyses too):
>>
>> bet - brain extract your T1
>>
>> flirt - register your T1 (brain extracted) to the MNI (brain extracted) with 12 DOF
>>
>> aff2rigid - create a 6 DOF matrix that will align the original T1 so that the mid-plane and ac-pc lines are aligned with the axes (using information from the MNI registration)
>>
>> flirt or applyXFM - apply the 6 DOF matrix from aff2rigid in order to resample your T1
>>
>> All the best,
>> Mark
>>
>>
>>
>>> On 25 Aug 2017, at 15:52, Alexandre Boutet <[log in to unmask]> wrote:
>>>
>>> Dear Fsl users,
>>>
>>> I would like to align FSPGR T1s scans with isotropic voxels to the ac-pc axial plane.
>>>
>>> Would anyone be able to direct me to an fsl command that does this? Or would anyone have a script that they could share?
>>>
>>> Thank you
>>>
>>> Alex
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