Hi Katie, thanks for sending the data.
In fact it looks like you did everything correct - it has run fine. The
zero voxel count in the log is just because you're not running full FLAME
I think.
If you view the stats/zstat* images you'll see that they look fine. You
just don't have anything passing the thresholding, because you're running
a mixed-effects analysis on only 4 time points, with 3 EVs, and it's clear
from cope1.hdr that your session/subject variability is very high.
So all is well - you might find that running fixed-effects on this shows
more group-level effect, or maybe you're planning on including more
timepoints, so maybe something will show up then.
Cheers, Steve.
On Wed, 29 Jun 2005, Karlsgodt, Katherine wrote:
> Hello,
> I'm doing an analysis comparing 2 datasets, where both were analyzed separately and registered to different study specific standard space brains. I have registered the relevant files from both datasets to avg152 space, and now want to compare them in a higher level analysis. Because I registered them myself and the directory structure is different, the "Inputs are 3D cope images from FEAT directories" option didn't work, because it thought that registration hadn't been carried out. I found another version of this question in the archives (http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind02&L=FSL&P=R35013&I=-3) and am trying to do what was recommended there.
>
> Basically, I have created a new directory structure as follows:
> for each subject a fake.feat file contains:
> -design.lev
> -mask.img & .hdr (I am only interested in one contrast, so this was made by binarizing the varcope that was in avg152 space)
> -example_func.img & .hdr (created from the standard space image, in this case avg152_T1brain)
> -a stats dir containing:
> -cope, varcope, tstat, zstat, neff, pe for the contrast of interest, all reg to avg152 space
>
> I have run a higher level analysis, and everything seems to be being
> read in just fine, and it goes through the entire process without
> errors, except that it says nmaskvoxels=0 and then Number of voxels=0.
> Since everything is registered to the same space, I'm not sure why the
> mask has no voxels- is it possible I need another file? I am not quite
> sure where I have gone wrong, and any advice would be much appreciated!
>
> thanks,
> Katie
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
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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