Hi - I'm guessing that this is just because this is not a first-level
analysis - see the comments on the Featquery manual stating that at
present the % calculations cannot be simply interpreted for higher-level
analyses.
Cheers, Steve.
On Mon, 12 Dec 2005, Eyleen Zhang wrote:
> Thanks, it's working now. But there still seems to be something wrong with
> the calculation.
> The thresh_zstat1 output seems reasonable. but the % estimate for pe & cope1
> are really strange. I've run featquery for the same set of data before, the
> % change is definitely not this huge.
>
> featdir image count min 10% mean median 90% max
> x (max) y (max) z (max)
> 1 filtered_func_data 1251897 -507.05 -32.49 7.14 4.73 50.36
> 489.68 44 80
> 23
> 1 stats/pe1 73641 -4333.52 -686.09 451.28 311.04
> 1800.86 6228.18 48 45 34
> 1 stats/cope1 73641 -4333.52 -686.09 451.28 311.04 1800.86
> 6228.18 48 45 34
> 1 thresh_zstat1 4936 0.00 2.36 2.74 2.64 3.26 4.84
> 25 38 26
> 1 thresh_zstat1_high 1060 0.00 3.04 3.33 3.24 3.75 4.84
> 25 38 26
>
> Here is the command I use for this output. The mask image is from the Brain
> Map VOI, corrected into avg152 matrix.
> featquery 1 cope1.feat 5 filtered_func_data stats/pe1 stats/cope1
> thresh_zstat1 thresh_zstat1_high -p -s
> masks/amygdala-mni-sym2.nii.gz
> so what's wrong here?
>
> On 12/11/05, Stephen Smith <[log in to unmask]> wrote:
> >
> > Hi - in that case just delete "reg" and then run featquery - then things
> > should run ok.
> >
> >
> >
> > On Sun, 11 Dec 2005, Eyleen Zhang wrote:
> >
> > > We've relocated all the analyses after a computer crash, and it seems
> > after
> > > that all the links of reg or reg_standard folder are gone.
> > > For now, I'm trying to run featquery on my third-level cross-subject
> > > analysis, so could the loweres space be bg_image.nii.gz?
> > > Thanks a lot.
> > > -Eyleen
> > >
> > >
> > > On 12/11/05, Stephen Smith <[log in to unmask]> wrote:
> > > >
> > > > Hi - if you had originally setup registration inside the FEAT GUI then
> > the
> > > > reg subdirectory would exist. You can run Featquery without the
> > > > registration information in the reg subdirectory - but in that case
> > the
> > > > input mask will have to be in the lowres space of the original FMRI
> > data.
> > > >
> > > > Cheers, Steve.
> > > >
> > > >
> > > > On Sat, 10 Dec 2005, Eyleen Zhang wrote:
> > > >
> > > > > Hi,
> > > > > I think I'm having the same problem here using featquery.
> > > > > Now that I can't fix those broken symbolic links, and there wasn't
> > even
> > > > an
> > > > > reg folder in my feat directory, is there any way I can still use
> > > > featquery
> > > > > to look at percent signal change? Perhaps by manually creating a reg
> > > > folder
> > > > > with the necessary registration info in it?
> > > > > Thanks.
> > > > > -Eyleen
> > > > >
> > > > >
> > > > > On 8/23/05, Stephen Smith <[log in to unmask]> wrote:
> > > > > >
> > > > > > This normally means that one of the files in the reg subdirectory,
> > or
> > > > one
> > > > > > of the symbolic links in there to files, has gotten broken. Can
> > you
> > > > do:
> > > > > >
> > > > > > avwinfo <featquerymaskimage>
> > > > > >
> > > > > > and then
> > > > > >
> > > > > > cd <featdir>/reg
> > > > > > avwinfo standard
> > > > > >
> > > > > > Cheers, Steve.
> > > > > >
> > > > > >
> > > > > > On Tue, 23 Aug 2005, Dost Ongur wrote:
> > > > > >
> > > > > > > Hello,
> > > > > > > I am using featquery to extract PEs from 30 FEAT directories. I
> > > > created
> > > > > > a
> > > > > > > mask in standard space (from a cluster of activation). When I
> > set
> > > > up
> > > > > > > featquery, it gives me the appropriate PE, COPE etc options so I
> > > > know it
> > > > > > is
> > > > > > > reading the design. But when I run it, I get an error message:
> > > > > > > "Error - mask size doesn't match any of the images in the FEAT
> > > > > > directory"
> > > > > > > before it even creates a Featquery directory.
> > > > > > >
> > > > > > > I know my mask is in standard space, I can overlay it on the
> > > > avg152T1
> > > > > > brain.
> > > > > > > Also, all of the FEAT directories have a reg/ directory with
> > the
> > > > > > > appropriate standard2example_func files etc.
> > > > > > >
> > > > > > > This is a procedure I have done hundreds of times in the past,
> > but
> > > > not
> > > > > > since
> > > > > > > installing FSL 3.2.
> > > > > > >
> > > > > > > What am I missing here?
> > > > > > >
> > > > > > > Thanks,
> > > > > > > Dost
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Eyleen Zhang
> > > > > Department of Psychology
> > > > > Brandeis University
> > > > > Waltham, MA 02454
> > > > >
> > > >
> > > > --
> > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > > Eyleen Zhang
> > > Department of Psychology
> > > Brandeis University
> > > Waltham, MA 02454
> > >
> >
> > --
> > 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
> >
>
>
>
> --
> Eyleen Zhang
> Department of Psychology
> Brandeis University
> Waltham, MA 02454
>
--
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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