Dear SPMers,
I would like to follow up on a discussion about coregistration started 
here: 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=SPM&P=R42697&m=21075. 

I have the same problem as Haakon, i.e. mean EPI badly coregistered to 
T1 in the Z direction for 3 out of 14 subjects, even when using phase 
maps in SPM8 unwarping.
I noticed that these problematic subjects seemed to be the ones with the 
most susceptibility artefacts, so I used Bas's wise advice and 
normalized my mean unwarped EPI the old fashioned way, i.e. on the EPI 
template. I felt happy at first, as it solved my coregistration problem 
for these subjects...
However I also noticed a strange phenomenon: using the old fashioned 
normalization seemed to reduce my artefacts in the OFC... which can't be 
! In fact I have the impression that in distorted EPIs this 
normalization process stretches the images to match the undistorted EPI 
template, and hence "creates" signal where there isn't (because of the 
artefacts). I attach an image showing the two normalization processes 
("new way" with coregistration of EPI on T1 and "old fashioned way" 
using the EPI template). I think that this stretching of the EPI is 
particularly evident at the bottom of the lateral ventricle, which is 
not well coregistered with the T1 scan when using the old fashioned way.
So I guess my question is: is it really a good idea to use this old 
fashioned normalization process when observing coregistration problems 
likely due to suceptibility artefacts ?
I apologize for the long e-mail, and will greatly appreciate any comment...
Thank you very much

Guillaume

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Guillaume Sescousse, PhD student
'Reward and decision making' group
Centre de Neuroscience Cognitive
CNRS UMR5229 - UCB Lyon 1
67 Bd Pinel, 69675 Bron, France

tel: 00 33 (0)4 37 91 12 44
fax: 00 33 (0)4 37 91 12 10
http://www.cnc.isc.cnrs.fr
http://www.isc.cnrs.fr/dre
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