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Subject:

Re: GLM (film_gls) and avwmaths -mas

From:

Stephen Smith <[log in to unmask]>

Reply-To:

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

Date:

Thu, 25 Nov 2004 10:10:46 +0000

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (68 lines)

Hi - it's just because this person isn't activating sufficiently strongly
according to your design. The "zeroing" of the zstat image isn't happening
at the point with avwmaths that you suggest; it is happening in the
cluster (thresholding) command slightly later, and the cluster that is
found isn't quite large enough to pass the probability test.

However, MELODIC does give plenty of visual activation, so it may just be
that your model isn't a great one?

Cheers.


On Wed, 24 Nov 2004, Bettyann Chodkowski wrote:

> hello all,
>
> i am trying to understand why the GLM analysis is unsuccessful (does
> not find any activation) for one subject but not for another.  i am
> walking thru the report.log files for both subjects and examining
> the output volumes.  i have put relevant files in this location:
>
> http://godzilla.kennedykrieger.org/~bettyann/fsl/
>
> where the directory 1345_2.feat contains the successful GLM analysis
> and directory kki_0006.feat contains unsuccessful GLM analysis.
>
> the analysis between the two subjects seems similar up until this
> step (from report.log):
>
> /usr/local/fsl/bin/avwmaths stats/zstat1 -mas mask thresh_zstat1
>
> the input volumes for avwmaths, stats/zstat1, have the following
> ranges:
>
> 1345_2 (successful)     = (-5.0684, 8.8195)
> kki_0006 (unsuccessful) = (-5.8488, 5.6056)
>
> the mask volumes look as expected with ranges of [0,1].  the output
> volumes, thresh_zstat1, differ and seem to be indicative of something
> going wrong.  the ranges are:
>
> 1345_2 (successful)     = (0, 8.8195)
> kki_0006 (unsuccessful) = (0, 0)
>
> i am confused as to what avwmaths <input> -mas <mask> <output> does.
> it seems to remove all negative values in addition to simply masking
> based on the output of the successful analysis.  but it seems to do
> more than that, given the output of the unsuccessful analysis.
>
> any ideas as to what is going on?
> thank you,
> - ba
> _____________________________________
> BettyAnn Chodkowski                       F.M. Kirby Center
> e: [log in to unmask]          Kennedy Krieger Institute
> v: 443.923.9524                           707 N. Broadway
> f: 443.923.9279                           Baltimore, MD, USA  21205
>

 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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