ah - sorry, yes - that's something that came up last week on the FSL list
- please see
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0211&L=fsl&T=0&F=&S=&P=7251
for the extra lines that do the masking.
Thanks, Steve.
On Wed, 27 Nov 2002, David Glahn wrote:
> Steve,
>
> Having looked at the easythresh code, the zstat image is never actually
> masked by the brain mask image. Is this an oversight?
>
> David
>
>
>
>
>
>
>
> On 11/26/02 9:53 AM, "Stephen Smith" <[log in to unmask]> wrote:
>
> > Hi - sorry, it's a very simple script (type more
> > /usr/local/fsl/bin/easythresh) mentioned in passing at
> >
> > http://www.fmrib.ox.ac.uk/fsl/feat5/programs.html
> >
> > just type easythresh to get the usage.
> >
> > Thanks, Steve.
> >
> >
> >
> > On Tue, 26 Nov 2002, David Glahn wrote:
> >
> >> Great, where could I find a discussion of easythresh, as it is not listed
> >> among the avwutils page?
> >>
> >>
> >> On 11/26/02 9:24 AM, "Stephen Smith" <[log in to unmask]> wrote:
> >>
> >>> Hi - are you wanting to do this inside FEAT (using the "pre-threshold
> >>> masking" option) or thresholding from the command-line using "easythresh"?
> >>> In the former case everything is taken care of for you - in the latter
> >>> case, if you put in the corrected (reduced) mask, then again it will be
> >>> taken care of for you.
> >>>
> >>> Regards, Steve.
> >>>
> >>> On Tue, 26 Nov 2002, David Glahn wrote:
> >>>
> >>>> Hello Everyone,
> >>>>
> >>>> I would like to use the cluster utility to threshold a tstat image that has
> >>>> been masked to only include a potion of the total image. Other than
> >>>> changing the volume option to reflect only the area included in the mask,
> >>>> what considerations should be taken?
> >>>>
> >>>> Best,
> >>>>
> >>>> David
> >>>>
> >>>> ________________________
> >>>> David Glahn, Ph.D.
> >>>> Department of Psychiatry and Research Imaging Center
> >>>> University of Texas, Health Science Center, San Antonio
> >>>> Voice (210) 567-5508
> >>>> Fax (210) 567-1291
> >>>>
> >>>
> >>> Stephen M. Smith
> >>> Head of Image Analysis, FMRIB
> >>>
> >>> 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
> >>>
> >>
> >>
> >> ________________________
> >> David Glahn, Ph.D.
> >> Department of Psychiatry and Research Imaging Center
> >> University of Texas, Health Science Center, San Antonio
> >> Voice (210) 567-5508
> >> Fax (210) 567-1291
> >>
> >
> > Stephen M. Smith
> > Head of Image Analysis, FMRIB
> >
> > 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
> >
>
>
> ________________________
> David Glahn, Ph.D.
> Department of Psychiatry and Research Imaging Center
> University of Texas, Health Science Center, San Antonio
> Voice (210) 567-5508
> Fax (210) 567-1291
>
Stephen M. Smith
Head of Image Analysis, FMRIB
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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