> So, if I extend what Paul wrote, the prescription looks as follows:
> Realign: Estimate & Reslice (Mean image only)
> Coreg: Estimate; source=SPGR, reference=EPI
> Coreg: Estimate; source=SPGR, reference=T1, other images = all EPIs
> (including mean)
> Normalize: Write; parameter file = *_sn.mat, Images to Write = EPIs, voxel
> size = [3,3,3]
> Normalize: Write; parameter file = *_sn.mat, Images to Write = SPGR, voxel
> size = [1,1,1]
> I just wanted to clarify few points in order to understand them
> 1. What is the role of realignment reslice for EPI images? All the images
> have the same voxel size. What exactly SPM reslices here and why I need to
> do it unless I do normalization afterwards? Is coreg reslice is virtually
> the same thing as realign reslice?
The reslicing from the realignment was just to produce an average of
all the realigned images. This average should be slightly better to
use for coregistration.
The actual reslicing done by coregistration and realignment is very
similar, but there may be some differences in terms of specific
settings. You can probably see what these are via the values set in
> 2. As some of you have pointed out that since my mean image had already been
> realigned with other EPI images, after I coregister SPGR source to mean
> image reference I do not have to take along the other EPIs. Does it mean
> that what happened is that after finding transformation parameters they were
> applied to the EPI images while no transformation should have been made?
If you move the SPGR into alignment with the mean EPI, and the mean
EPI is in alignment with all the other EPI images, then the SPGR
should also be aligned with the other EPI.
The transformation parameters are applied to the source image (and any
other images), whereas the reference image is untouched.
> On Tue, Dec 21, 2010 at 1:36 PM, Paul Wright <[log in to unmask]> wrote:
>> Hi John,
>> The reason your images are misaligned after coregistration is that you got
>> the source and reference images the wrong way around: you move the SPGR
>> source to fit the mean EPI reference, and the apply the transformation to
>> the other EPIs. This mean that
>> a) the structural and EPIs will still be in the same relative positions:
>> if they began unaligned, they will stay unaligned
>> b) the EPIs will no longer be in register with the mean EPI
>> I think you wanted to move the mean EPI source to fit the SPGR reference,
>> and then move the other EPIs along with it. However, as others have already
>> said a more straightforward approach would be to coregister the SPGR with
>> the mean EPI (leaving the other EPIs alone). You can subsequently use your
>> normalisation parameters on both sets of images.
>> This approach holds also using Marko's additional initial coregistration
>> of the structural to the T1 template, which is intended to improve
>> segmentation. This would go in between the SPGR-EPI coregistration and
>> 1) Realignment
>> 2) Coregister SPGR source to EPI reference
>> 3) [Optional] Coregister SPGR source to T1 template reference, taking
>> along EPIs as other images
>> 4) Normalisation / segmentation
>> 5) Write normalisation parameters for SPGR and EPIs.
>> Hope this helps,