Hi Bertram,
have you tried it? The impact of the first volume on the mean one might
not be as apparent anymore. This may not be optimal but for
consistency's sake in a group study may be a worthwhile approach.
If not, you could of course remove the first few volumes for all, or
simply specify the second (third...) volume twice when selecting the
images, but again, I would be worried if this is in a group context as
any special treatment to one subject has the potential to bias the group
result.
Also note that the first volume in a subject's second session will
initially be registered to the first/mean of the first session, so this
will also come into play...
Cheers
Marko
Bertram Walter wrote:
> 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
>>>
>>
>
>
--
____________________________________________________
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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