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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