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
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