Hi Marco,
but what's the best way if the first volume is severely distorted by
motion during the scan? The first realignment step would use a bad volume
with unpredictable results on the final mean reference. Doing the first
step with a good reference could be a solution. But how can I do it in SPM?
Cheers,
Bertram
On Tue, 27 Jun 2017 11:00:32 +0200, Marko Wilke
<[log in to unmask]> wrote:
> 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
>>
>
--
Dr. Bertram Walter
Bender Institute of Neuroimaging
University of Giessen
Otto-Behaghel-Str. 10H
35394 Giessen
Germany
Phone +49 (641) 99-26307
or +49 (641) 99-26331 (Secretary)
Fax +49 (641) 99-26309
www.bion.de
