Try the attached function.
best regards,
-John
On 28 October 2010 17:29, lion gao <[log in to unmask]> wrote:
> Dear all,
>
> I find these answer are quite useful to me as well. However, one
> additional question i have is that after the T1 or other images are
> re-orietated, I can see the difference in SPM display. But when I open
> it with MRIcro or ImageJ, it seems there is no change at all. I wander
> whether there is way to save the reorientated images so that MRIcro
> especially ImageJ can open it with new position.
> Thank you very much in advance!
>
> Best wishes,
> Gao
>
>
> On 28 October 2010 23:18, Kiyotaka Nemoto <[log in to unmask]> wrote:
>> Dear Christiane,
>>
>> You can get the script "auto_reorient.m" from the following link.
>>
>> http://www.nemotos.net/?p=122
>>
>> Hope this helps,
>>
>> Kiyotaka
>>
>> On Thu, 28 Oct 2010 15:37:51 +0200
>> michel grothe <[log in to unmask]> wrote:
>>
>>>
>>> There is also a script called 'auto_reorient.m' somewhere in the archives of the mailing-list, that coregisters your images to the T1-template.
>>>
>>> Best,
>>> Michel
>>>
>>> > Date: Thu, 28 Oct 2010 13:56:04 +0100
>>> > From: [log in to unmask]
>>> > Subject: Re: [SPM] Anterior commissure
>>> > To: [log in to unmask]
>>> >
>>> > Hi Christiane
>>> >
>>> > It also usually works reasonably well to coregister a structural image
>>> > to the T1 template (i.e., run coregister:estimate, set the template
>>> > avg152T1.nii as the reference, and the T1 structural as the source
>>> > image).
>>> >
>>> > Hope this helps,
>>> > Jonathan
>>> >
>>> > On Thu, Oct 28, 2010 at 12:39 PM, John Ashburner <[log in to unmask]> wrote:
>>> > > Scans do not need to be exactly aligned with the AC at 0,0,0. They
>>> > > only need to be (roughly) within about 3cm and 15 degrees. If all
>>> > > your subjects are positioned in roughly the same way, then you can
>>> > > figure out a suitable set of rotations and translations and apply them
>>> > > to all data.
>>> > >
>>> > > Best regards,
>>> > > -John
>>> > >
>>> > > On 28 October 2010 11:24, Christiane Moller <[log in to unmask]> wrote:
>>> > >> Hallo,
>>> > >>
>>> > >> I'm nieuw to SPM and I wonder if there is a tool with which you can align the T1 scans automatically around the anterior commissure instead of doing this by hand. I have a lot of scans and this would take me a lot of time.
>>> > >> I would be very greatful for some help.
>>> > >>
>>> > >> Thanks.
>>> > >>
>>> > >> Christiane
>>> > >>
>>> > >
>>>
>>
>> ----------------
>> Kiyotaka Nemoto, M.D.
>> Department of Psychiatry
>> Graduate School of Comprehensive Human Sciences
>> University of Tsukuba
>> 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
>> E-mail: [log in to unmask]
>>
>
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