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Subject:

Re: AW: [FSL] Timeseries in FSL view

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 21 Dec 2004 09:06:00 +0000

Content-Type:

text/plain

Parts/Attachments:

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text/plain (87 lines)

Hi,

You might find our brief technical report and the references
in that (particularly Kiebel et al 1999) to be useful in
explaining exactly what GRF does. The report is at:
   
http://www.fmrib.ox.ac.uk/analysis/techrep/tr00df1/tr00df1/tr00df1.html

Matthew Brett also has an excellent web page explaining GRF
and cluster-based inference at:
   http://www.mrc-cbu.cam.ac.uk/Imaging/Common/randomfields.shtml

Hope these help.
All the best,
        Mark


On 21 Dec 2004, at 00:07, Fornito, Alexander wrote:

> That worked -thanks!
> You're answer raised another issue for me. I'm still trying to
> understand how thresholding is achieved in FEAT. Let me see if I
> understand...
> For voxel-based thresholding, is each voxel treated independently?
> Is the corrected p-value set by the user corrected according to GRF
> theory (eg., if I set the value to .05, the threshold is corresponds
> to a GRF corrected .05. In this case, is there any way of determining
> what the actual threshold is?
> For cluster-based thresholding, are the voxels smoothed according to
> the FWHM set in the pre-stats tab of the FEAT GUI? Thus, for eg., if
> the FWHM is 5mm then the stats are run on clusters of 5 or more
> contiguous voxels?
> What do the Z values and p values represent in cluster based
> thresholding, and are there any rules of thumb for determining what
> the appropriate values for these are?
> Once again, many thanks for your assistance,
> Alex
>
>
> -----Original Message-----
> From: Andreas Bartsch [mailto:[log in to unmask]]
> Sent: Monday, December 20, 2004 8:01 PM
> To: [log in to unmask]
> Subject: [FSL] AW: [FSL] Timeseries in FSL view
>
> Hi Alex,
> ok - this one is easy:
> Load the 4D-file (e.g., filtered_func_data) into FSLView. The selected
> file appears in the lower box on the left. Once you have loaded the
> stats image (e.g., thresh_zstat1) you need to select the 4D-file in
> the box again to view the time series. I assume you had the stats
> image selected (which is 3D), so you could not access the time series
> of the 4D file.
> And yes - all clusters surviving the threshold are listed. But note
> that are always some stipulations involved in defining what is
> regarded as a cluster (which depend on the precise approach chosen).
> To define contiguous clusters, FEAT applies an initial Z-threshold you
> choose.
> Best regards-
> Andreas
>
> -----Ursprüngliche Nachricht-----
> Von: Alex Fornito [mailto:[log in to unmask]]
> Gesendet: Mo 20.12.2004 03:39
> An: [log in to unmask]
> Cc:
> Betreff: [FSL] Timeseries in FSL view
>
>
>
> Hi,
> I'm having trouble accessing timeseries data in FSL view.
> I load the 4D image, and add the thresh_zstat image for the
> contrast of
> interest. The stat image gets overlaid on the 4D image, but I
> am uable o
> select "Timeseries" from the "View" menu. Am I missing
> something?
> Also, as an aside, in the report.html page, do the cluster
> lists obtaine
> by clicking on a contrast image represent an exhaustive list
> of all
> clusters that syurvived thresholding?
> Many thanks for your help,
> Alex
>

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