Hi,
The command cluster does both - it calculates the cluster
images and it can also perform GRF calculations. I'm not
sure why this is amazing. If you are going to do GRF
calculations then you need to give is a smoothness
estimate via the option:
-d,--dlh smoothness estimate = sqrt(det(Lambda))
which you can get from the program smoothest.
In order to get the GRF output you need to produce an
appropriate output such as --opvals or --minclustersize
I hope this is clearer.
All the best,
Mark
On 17 Feb 2010, at 08:57, Niklas Stein wrote:
> Hi Steve,
>
> thanks for your reply. My question refers to the command
> '$FSLDIR/bin/cluster'. My impression is that it just puts out a
> cluster
> list of (face, edge or vertex?) adjacent voxels, but the website
> states
> that it uses GRF, which I am amazed of. Therefore, I was wondering
> whether the output from e.g. 'cluster -i stat_vox_p_tstat<n> -t .95'
> includes any kind of GRF based correction or if the website is
> misleading here.
>
> Cheers,
> Niklas
>
> Stephen Smith wrote:
>> Hi - there's a little more info in the FEAT manual
>> http://fsl.fmrib.ox.ac.uk/fsl/feat5/detail.html#poststats
>> FEAT offers both voxel-based and cluster-based thresholding, in
>> both cases the test statistic (voxel Z value and cluster size
>> respectively) are turned into corrected p-values using GRF
>> theory. Not sure if that answers your question - but hopefully
>> it's a pointer in the right direction. For a lot more useful
>> stuff on GRF see the Cambridge Imagers website.
>> Cheers.
>> On 16 Feb 2010, at 12:02, Niklas Stein wrote:
>>> Hi experts,
>>>
>>> on the individual tools' documentation pages, for inference
>>> 'cluster' is
>>> documented as 'cluster-based thresholding using GRF theory for
>>> inference'. I was wondering, how (and why) GRF is incorporated into
>>> 'cluster' and whether 'cluster' has any other purpose than giving
>>> a list
>>> of clusters by thresholding output from randomise.
>>> Please do not laugh at the potential sillyness of my question, but
>>> since
>>> the documentation is sparse and it is listed as an inference tool
>>> I feel
>>> in need for clarification.
>>>
>>> Cheers,
>>> Niklas
>>>
>>>
>>> --
>>> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und
>>> Genossenschaftsregister sowie das Unternehmensregister (EHUG):
>>>
>>> Universitätsklinikum Hamburg-Eppendorf
>>> Körperschaft des öffentlichen Rechts
>>> Gerichtsstand: Hamburg
>>>
>>> Vorstandsmitglieder:
>>> Prof. Dr. Jörg F. Debatin (Vorsitzender)
>>> Dr. Alexander Kirstein
>>> Prof. Dr. Dr. Uwe Koch-Gromus
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>
>
> --
> ----------------------------------------------------------------------
> Dipl.-Phys. Niklas Stein
> ----------------------------------------------------------------------
> Institut für Systemische Neurowissenschaften
> Universitätsklinikum Hamburg-Eppendorf
> Martinistr. 52, Haus W34
> D-20246 Hamburg, Germany
> Tel.: +49-40-7410-57882
> Fax.: +49-40-7410-59955
> mail: [log in to unmask]
> http:/www.uke.uni-hamburg.de/institute/systemische-neurowissenschaften
> ----------------------------------------------------------------------
> Time ferðast mun hafa gert flóknari málfræði.
> ----------------------------------------------------------------------
> () ascii ribbon campaign (http://arc.pasp.de)
> /\ * against html mail and vcards *
> ----------------------------------------------------------------------
> Please avoid sending me Microsoft Office files as attachments.
> (see http://www.gnu.org/philosophy/no-word-attachments.html)
> ----------------------------------------------------------------------
>
>
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und
> Genossenschaftsregister sowie das Unternehmensregister (EHUG):
>
> Universitätsklinikum Hamburg-Eppendorf
> Körperschaft des öffentlichen Rechts
> Gerichtsstand: Hamburg
>
> Vorstandsmitglieder:
> Prof. Dr. Jörg F. Debatin (Vorsitzender)
> Dr. Alexander Kirstein
> Prof. Dr. Dr. Uwe Koch-Gromus
|