Hi Christian's right when it comes to feeding in data from first-level
analyses. However, if you are feeding in standard-space copes (eg from a
second-level anlaysis) into FEAT then what group-FEAT does is:
1) assumes that the copes are in the "stats" subdirectory in a feat
directory. this way it knows to look in the feat directory itself for
things like the mask image etc.
2) it thinks that the data is already in standard space because it was
a second-level analysis if the "design.lev" file exists in the FEAT
directory - so you might want to create this if you have generated this
data some other way.
3) now, when you did a second level analysis, the standard space versions
of the mask image and the stats images get put in a reg_standard
directory. to keep things easy for higher-than-second-level anlaysis, the
second-level feat directory has a link in the feat called reg_standard
pointing simply straight back into the feat directory, so that when it
looks for standard space stuff "in reg_standard" it finds all the files
(which are already in standard space). moral of the story is - you might
need to create that link, ie in the "second-level" feat directory, do
ln -s . reg_standard
sorry this sounds copmlicated - but the whole thing is designed so that
for users doing standard analyses these kind of details are taken care of
automatically.
maybe we should prepare a more detailed clear version of the above to add
to the manual.
please email again if this doesn't cover what you are trying to do!
Thanks, Steve
On Thu, 10 Oct 2002, Stanley Colcombe wrote:
> Hi All-
> This is probably a simple oversight on my end. I'm trying to use FLAME to
> analyze some existing cope images that are already registered to MNI space.
> However, after setting up the parameters in the model, FLAME gives me the
> following message:
> "Registration has not been run for all of the FEAT directories that you have
> selected for group analysis. Please turn on and setup registration."
> I do have "Inputs are cope images" selected in the "Data" tab. What am I
> missing?
> Thanks in advance.
> Stan.
>
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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