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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.


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> 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