Hi Bertram,
in the batch interface, there is actually a setting for this ("Register
to first" or "Register to mean"). In the latter case, there will
basically be a two step procedure: registering all images to the first,
create mean, then register all images to this one. You should also be
able to implement this on the command line, passing a 'rtm' flag to
spm_realign. In neither case should you have to manually edit the file
order to achieve this.
Cheers
Marko
Bertram Walter wrote:
> Dear all,
>
> I want to use the middle volume of my functional scan as reference scan
> for realignment in realign & unwarp. In the manual it is mentioned
>
> "The first image in the list specified by the user is used as a reference
> to which all subsequent scans are realigned. The reference scan does not
> have to the the first chronologically and it may be wise to chose a
> "representative scan" in this role."
>
> My question: How do I have to specify the scans in realign&unwarp?
>
> E.g. if I have 10 scans and want to use scan # 5 as reference
>
> Option A: When entering 10 scans in the sequence
> 5 1 2 3 4 6 7 8 9 10
> I get realignment parameters for 10 volumes
>
> 0.0000000e+00 -1.4331259e-14 1.2492012e-14 9.6730144e-19
> 1.1186837e-16 2.6148260e-17
> 1.2853422e-01 8.9730393e-02 3.6775770e-02 -9.4771013e-06
> -3.2223731e-04 1.4239692e-03
> 4.6301388e-02 -5.0520113e-02 -6.9045253e-02 -6.6616240e-04
> -2.1641583e-05 5.6118550e-04
> 4.6174405e-02 7.0661590e-02 8.4805501e-02 3.6093835e-04
> 3.1108790e-04 8.4482913e-05
> 2.1246018e-02 1.2126505e-02 2.8272003e-02 -9.6548672e-04
> -2.1787263e-04 2.5528354e-04
> 4.2798897e-02 9.4051293e-02 1.7265070e-01 -1.0246176e-03
> -1.2925461e-04 2.8213895e-04
> 1.1362071e-02 6.6483921e-03 7.1757735e-02 -8.6840762e-04
> -1.9301134e-04 -2.7897976e-04
> 9.8239930e-03 8.1840421e-02 1.2797305e-01 5.9959604e-04
> 2.9641170e-04 -5.0873017e-04
> 1.4794704e-02 9.1027866e-02 9.7297841e-02 5.4889707e-04
> -9.8659697e-05 -5.5278722e-04
> 9.3970797e-03 1.1272641e-01 1.2209011e-01 3.9738355e-04
> 5.6547393e-05 -8.0964723e-04
>
> The first line refers to scan no 5, right?
> The resampled nifti contains 10 volumes
>
> Option B: When entering 11 scans in the sequence
> 5 1 2 3 4 5 6 7 8 9 10
> I get realignment parameters for 11 volumes
>
> 0.0000000e+00 -1.4331259e-14 1.2492012e-14 9.6730144e-19
> 1.1186837e-16 2.6148260e-17
> 1.2853422e-01 8.9730393e-02 3.6775770e-02 -9.4771013e-06
> -3.2223731e-04 1.4239692e-03
> 4.6301388e-02 -5.0520113e-02 -6.9045253e-02 -6.6616240e-04
> -2.1641583e-05 5.6118550e-04
> 4.6174405e-02 7.0661590e-02 8.4805501e-02 3.6093835e-04
> 3.1108790e-04 8.4482913e-05
> 2.1246018e-02 1.2126505e-02 2.8272003e-02 -9.6548672e-04
> -2.1787263e-04 2.5528354e-04
> -1.1166691e-14 -5.5177401e-15 1.2492012e-14 -5.7451305e-17
> 2.3912931e-16 2.4868550e-17
> 4.2798897e-02 9.4051293e-02 1.7265070e-01 -1.0246176e-03
> -1.2925461e-04 2.8213895e-04
> 1.1362071e-02 6.6483921e-03 7.1757735e-02 -8.6840762e-04
> -1.9301134e-04 -2.7897976e-04
> 9.8239930e-03 8.1840421e-02 1.2797305e-01 5.9959604e-04
> 2.9641170e-04 -5.0873017e-04
> 1.4794704e-02 9.1027866e-02 9.7297841e-02 5.4889707e-04
> -9.8659697e-05 -5.5278722e-04
> 9.3970797e-03 1.1272641e-01 1.2209011e-01 3.9738355e-04
> 5.6547393e-05 -8.0964723e-04
>
> The first line and the sixth line refer to scan no 5, right?
> The resampled nifti contains again 10 volumes and differs slightly from
> the nifti resulting from option A.
>
> Which version should be used?
>
> Many thanx,
>
> Bertram
>
--
____________________________________________________
Prof. Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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