Dear Andy,
> For this script to work, how can we specify the file directory so that it
> knows where to find the img files?
You don't have to specify the directory beforehand. running script
brings GUI file selector of SPM, so you just choose whatever images
you want.
> And may I know if this script also corrects rotation as well? Or just
> correct [0 0 0] to AC.
It does rigid body transformation, so corrects rotation as well.
Best regards,
Kiyotaka
> On Tue, Feb 10, 2015 at 6:49 AM, Kiyotaka Nemoto <[log in to unmask]>
> wrote:
>>
>> Hi Silke,
>>
>> You can find a script which enables what you want on SPM ML archive.
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;d1f675f1.0810
>>
>> It needs a slight modification, so I modified it and made it available
>> as auto_reorient.m from the link below.
>>
>> http://www.nemotos.net/?p=17
>>
>> I always use it and it works for even 1000+ images. It takes a few
>> minutes per subject though.
>>
>> Hope this helps,
>>
>> Kiyotaka
>>
>>
>> 2015-02-09 22:59 GMT+09:00 Matura, Silke Dr. Dipl.-Psych.
>> <[log in to unmask]>:
>> > Dear all,
>> >
>> > I am planning to do voxel-based morphometry with a large data set ( n =
>> > 180
>> > anatomical scans). Since manual re-orientation of all images would be
>> > very
>> > time consuming, I am currently looking for a way to automatise this
>> > step. I
>> > have read in the SPM archives that coregistration of the individual
>> > scans to
>> > a template would be one solution to circumvent manual re-orientation.
>> > I
>> > have tried coregistering the individual scans to the T1 template
>> > provided by
>> > SPM8 (T1.nii). When I click on the AC in the resulting re-oriented
>> > images,
>> > the mm coordinates significantly differ from a position close to 0,0,0.
>> > So
>> > here are my questions:
>> >
>> > 1.) Is the T1 template provided by SPM8 ideal for coregistration?
>> >
>> > 2.) Are there better ways for automatic reorientation than coregistering
>> > the
>> > anatomical scans to a template ?
>> >
>> > I am looking forward to your answers.
>> >
>> > Thank you!
>> >
>> > Silke
>> >
>> > --
>> > Dr. Dipl.-Psych. Silke Matura
>> > Arbeitsbereich Altersmedizin / Geriatric Medicine
>> > Institut für Allgemeinmedizin / Institute of General Practice
>> > Goethe Universität Frankfurt a.M./
>> > Goethe University Frankfurt a.M.
>> > Theodor-Stern-Kai 7
>> > D-60590 Frankfurt
>> > Tel.: ++49-(0)69-6301-6476
>> > Fax.: ++49-(0)69-6301-6428
>> > eMail: [log in to unmask]
>> > Homepage: http://www.allgemeinmedizin.uni-frankfurt.de
>> > http://www.allgemeinmedizin.uni-frankfurt.de/tda/tda.html
>>
>>
>>
>> --
>> Kiyotaka Nemoto, M.D., Ph.D.
>> Assistant Professor
>> Department of Psychiatry
>> Division of Clinical Medicine, Faculty of Medicine
>> University of Tsukuba
>> 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
>> E-mail: [log in to unmask]
>
>
--
Kiyotaka Nemoto, M.D., Ph.D.
Assistant Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: [log in to unmask]
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