Hello Johanna, yes, your questions make sense.
When you run a first-level FEAT analysis (including registration), the
registration information (ie transforms) all get created, and saved in the
reg subdirectory. However, the various images (cope, example_func, highres
etc) do not get resampled to standard space UNTIL you either run a
higher-level analysis or UNLESS you explicitly make this happen with
"featregapply" (see below). This is to save disk space.
So - in your case, to get those images in reg_standard, just take an
existing FEAT directory and run
featregapply <featdirectoryname.feat>
thanks, Steve.
On Tue, 1 Jul 2003, Johanna Pekkola wrote:
> Hello!
>
> And thanks for the advice last time.
> Now I´d have a question about the way FEAT writes registration files.
>
> To view the cope data overlayed on the same subjects high-resolution scans
> in the standard space I´ve opened
>
> experiment.feat/reg_standard/reg/highres.hdr
>
> and overlayed
>
> experiment.feat/reg_standard/stats/cope1.hdr.
>
> Now, to my surprise, when I run analyses sometimes the reg_standard
> directory does not appear at all in the feat directory - not even if I have run
> registration of the 4D volume via T1 highres to standard space and in the
> report page registration seems good all the way.
>
> In these cases I´ve tried to open highres.hdr in the reg directory and overlay
> cope1.hdr from the stats directory, not successfully.
>
> So - my question: should there always be a reg_standard directory if
> registration has been run to standard space? Is there a choice to about it
> I´ve missed?
>
> Thanks,
> Johanna Pekkola
> TKK/LCE
> Finland
>
Stephen M. Smith MA DPhil CEng MIEE
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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