Hi again,
> I think the images I have fed into the processing pipeline look very
> good. Is it possible to send you some examples for your comment?
> Which ones would be most helpful for review?
what do you mean by "fed into"? Do you mean your original images, or
do you mean the *_brain.* images you get after the fslvbm_1_bet step?
If you have not checked the *_brain.* images I suggest you do so,
looking for signs of brain being eroded or of non-brain being left in.
If that looks good your next step should be to have a look at the
template_GM_4D file to see how the registration has succeeded.
If you still cannot find the source of the problem you can put all the
*_brain.* images into a 4D file with the command
fslmerge -t ForJesper `echo *_brain.*`
If the resulting ForJesper file is not too large you can then upload
it to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and email me the reference number. If it is very big you can change
the fslmerge command above to only include a few of the *_brain.* files.
Jesper
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