Many thanks for the response and suggestion - I have posted to the Freesurfer list as well.
We're a little confused - I guess we naively thought, given the way we've exported our 2-D structural and functional data out of Freesurfer, that FSL would treat it as if it was single-slice data. The FSL FAQ online says that FEAT will work with single-slice data just like normal multi-slice data.
Again, if anybody has any suggestions or has performed FEAT analyses on functional data projected to the hemispheric surface suing Freesurfer, please let me know.
Thanks,
Susan MCL
On Wed, 11 Mar 2009, Steve Smith wrote:
> Hi,
>
> Good point - I'm not sure where that page has disappeared to. We'll chase this
> up....it might be worth posting this question to the FreeSurfer list too
> though.
> FEAT will be unhappy at higher-level if you haven't done registration at lower
> level with FEAT to a standard space image.
>
> Cheers.
>
>
>
> On 10 Mar 2009, at 23:33, Susan McLaughlin wrote:
>
>> Hi,
>>
>> An FSL/Freesurfer newbie question:
>>
>> We are conducting analyses of functional data extracted to the brain surface
>> (by Freesurfer), registered to that surface.
>>
>> I am first performing lower-level FSL analyses of single-subject, single-run
>> data using the Freesurfer surface functional data (converted back to
>> Nifti). I always get same error message when I enter the functional surface
>> input (“Warning – have auto-set BET preprocessing option and/or
>> registration
>> DOF on the basis of image fields-of-view; check settings”), but I have
>> been
>> ignoring this message and the analysis seems to run fine.
>>
>> However, when I try to run a higher-level analysis across sessions using the
>> lower-level FEATs, I always get another error 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”) and the analysis won’t
>> run. This occurs regardless of whether my lower-level analyses are
>> registered to the extracted surface structural, to the extracted surface
>> functional, or with registration turned off.
>>
>> Searching the FSL list, I see others have had this problem (back in 2005),
>> but it appears the solution promised at
>> http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html cannot be accessed as
>> that URL is no longer active.
>>
>> Any suggestions?
>>
>> Sorry for the somewhat simplistic question.
>>
>> Susan McLaughlin
>> Department of Speech & Hearing Sciences
>> University of Washington
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
Susan McLaughlin
Doctoral Student
Dept. of Speech and Hearing Sciences
University of Washington
1417 NE 42nd St.
Seattle, WA 98105
Phone: 206-850-8638
Fax: 206-543-1093
Email: [log in to unmask]
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