This message is both for SPM and MEDx users.
We have a study for which we used MEDx implementation of AIR for
realignment (rather than SPM'96 realign module), and now we are trying to
replicate the 2-step realignment in MEDx. Here are my questions:
1) In SPM'96, when the 1st realignment is done, the images normally do not
get resliced, and only the mean image is produced. I presume that the mean
image must reflect realignment of Scan 2 to Scan 1 even though rScan2 is
not produced. Am I correct?
2) Because the 1st realignment will create a Scan2.mat file, the 2nd
realignment will see it and use it when realigning Scan 1 and Scan 2 to
the mean. But the mean is already very close to Scan 1 and "realigned
Scan 2". What would change if I delete Scan2.mat file and realign original
Scan 1 and Scan 2 to the mean?
On April 6, Dr. Jesper Andersson wrote in response to a similar question:
>> There are several reasons why it is a good idea to align images to a
>> "first pass mean image" rather than just the first image. 1. PET data
>> are typically quite noisy and all registration methods are negatively
>> affected by noise. By realigning to a mean image rather than to a
>> single image, the noise properties improve.
>> 2. The realignment in SPM96 will perform 8 iterations, which will be
>> sufficient most of the time but may in the event of large movements be
>> a tad bit on the small side.
>> 3. In SPM96 a small angle approximation (sin(a) ~ a) is used when
>> estimating the effects of rotations. Again, this is perfectly fine when
>> movements are small but may be a problem for larger movements. 2 and 3
>> both benefit from performing a second run of the realignment, provided
>> that the .mat files from the first realignment is used.
>> By deleting the .mat files from the first pass you still have the
>> benefits from point 1, but loose the potential benefits from points 2
>> and 3. My personal guess would be that provided that movements are in
>> the range one typically see for intrasession realignment (a couple of
>> mm) you don't need to worry even if you delete the .mat files from the
>> first session.
I am realigning scans that were acquired on different days. Does that mean
that I should be careful with the .mat files from the 1st realignment (or
with resliced images that MEDx writes)?
Any help would be greatly appreciated --
Brain Imaging Laboratory
New York State Psychiatric Institute
New York, NY