Hi - sure, re-upload once you're done.
Cheers.
On Thu, 15 Dec 2005, Cherif Sahyoun wrote:
> Hey Steve!
>
> My bad. Dunno how I let that through...
> I fixed it and started to rerun the analysis, and the same errors are still
> showing up!
>
> Shall I upload the directory again when it's done?
>
> best,
> cherif
>
> On 12/14/05, Stephen Smith <[log in to unmask]> wrote:
> >
> > Hi Cherif - user-error I'm afraid ;-)
> >
> > Your first timepoint isn't being modelled - hence the model-fitting is
> > pretty unhappy! If you don't want to model the first timepoint then just
> > exclude it from the analysis, or give it it's own EV.
> >
> > Cheers, Steve.
> >
> >
> >
> >
> > On Wed, 14 Dec 2005, Cherif Sahyoun wrote:
> >
> > > Hey Steve!
> > >
> > > Thx!
> > > It's uploaded with ID 904366 as grp_cope_better.gfeat.tar.gz
> > >
> > > best,
> > > cherif
> > >
> > > On 12/13/05, Stephen Smith <[log in to unmask]> wrote:
> > > >
> > > > Hi - in this case the outliers may be subtle - if you want to send
> > your
> > > > data (the complete .gfeat directory) we can have a quick look:
> > > >
> > > > Please upload the files in a single compressed tarfile to
> > > > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> > > > and then email me the upload ID.
> > > >
> > > > Cheers.
> > > >
> > > >
> > > > On Mon, 12 Dec 2005, Cherif Sahyoun wrote:
> > > >
> > > > > Hey Steve!
> > > > >
> > > > > done that. no luck... no ouliers outside the brain, and looking at
> > the
> > > > > timecourses, no voxel seems to be much different from its
> > neighbours...
> > > > > Anything in particular I am looking for? I may be looking at the
> > file
> > > > wrong,
> > > > > but it looks fine to me... what else could the problem be?
> > > > >
> > > > > thx,
> > > > > cherif
> > > > >
> > > > > On 12/12/05, Stephen Smith <[log in to unmask]> wrote:
> > > > > >
> > > > > > Hi - you should probably set the colour lookuptable to Greyscale
> > and
> > > > the
> > > > > > display range to whatever
> > > > > > avwstats++ <fmridata> -r
> > > > > > shows. Then flick through the timepoints and also turn on
> > timeseries
> > > > > > viewing in order to see strong outliers easily.
> > > > > >
> > > > > > Cheers.
> > > > > >
> > > > > >
> > > > > > On Sun, 11 Dec 2005, Cherif Sahyoun wrote:
> > > > > >
> > > > > > > Hey Steve!
> > > > > > >
> > > > > > > Ok, I opened a bunch of copes in fslview. I don't have other
> > data
> > > > handy,
> > > > > > so
> > > > > > > i don't know if that's normal, but the background for all copes
> > is a
> > > > > > uniform
> > > > > > > "orange", along the same tones as inside the brain... should it
> > be
> > > > > > "black"
> > > > > > > i.e. nothing there compared with the brain (which goes from
> > > > > > > yellow-orange-red)?
> > > > > > > Also, on a few of the copes, on the edge of the brain usually,
> > there
> > > > are
> > > > > > a
> > > > > > > couple of point that go down to "black" (individual pixels,
> > usually
> > > > only
> > > > > > > 1/cope image).
> > > > > > >
> > > > > > > Does that help hone in on the problem?
> > > > > > >
> > > > > > > thx,
> > > > > > > cherif
> > > > > > >
> > > > > > > On 12/10/05, Stephen Smith <[log in to unmask]> wrote:
> > > > > > > >
> > > > > > > > Hi - no, ignore the FLIRT warnings.
> > > > > > > >
> > > > > > > > The FLAME warnings are of more concern - this almost always
> > means
> > > > that
> > > > > > you
> > > > > > > > have very strong outliers in your data input to FLAME. One
> > thing
> > > > to
> > > > > > check
> > > > > > > > is to load the .gfeat/cope? images into fslview and flick
> > through
> > > > the
> > > > > > > > timepoints to check for outliers.
> > > > > > > >
> > > > > > > > Cheers, Steve.
> > > > > > > >
> > > > > > > >
> > > > > > > > On Fri, 9 Dec 2005, Cherif Sahyoun wrote:
> > > > > > > >
> > > > > > > > > Hi!
> > > > > > > > >
> > > > > > > > > 2 errors I am getting when running high level analyses in
> > Feat:
> > > > > > > > > - same as in my previous email, everytime flirt is called, I
> > get
> > > > an
> > > > > > > > error
> > > > > > > > > stating
> > > > > > > > > WARNING: Both reference and input images have an sform
> > matrix
> > > > set
> > > > > > > > > The output image will use the transformed sform from the
> > > > reference
> > > > > > image
> > > > > > > > > This happens both in low level and high level analyses (more
> > > > details
> > > > > > in
> > > > > > > > my
> > > > > > > > > previous message)
> > > > > > > > >
> > > > > > > > > the reason I am repeating this is it may be related to the
> > > > following
> > > > > > > > > warnings I get in high level stats:
> > > > > > > > >
> > > > > > > > > WARNING: FLAME stage 2 has given an abnormally large
> > difference
> > > > to
> > > > > > stage
> > > > > > > > 1
> > > > > > > > > x=50,y=92,z=41
> > > > > > > > > vox=173818
> > > > > > > > > zts[0](vox)=7.7325
> > > > > > > > > zemlowerts[0](vox)=4.62063
> > > > > > > > > beta_mean[0](vox)=2.73318e-05
> > > > > > > > > beta_b[0](vox)/beta_c[0](vox)=1.00022e-10
> > > > > > > > >
> > > > > > > > > WARNING: FLAME stage 2 has given an abnormally large
> > difference
> > > > to
> > > > > > stage
> > > > > > > > 1
> > > > > > > > > x=50,y=92,z=42
> > > > > > > > > vox=173819
> > > > > > > > > zts[0](vox)=7.99212
> > > > > > > > > zemlowerts[0](vox)=4.7153
> > > > > > > > > beta_mean[0](vox)=2.73318e-05
> > > > > > > > > beta_b[0](vox)/beta_c[0](vox)=1.00022e-10
> > > > > > > > >
> > > > > > > > > I get MANY iterations like these before the analysis finally
> > > > ends
> > > > > > (in
> > > > > > > > > >24hrs!), and am not sure at all what this means or if it's
> > > > > > normal...
> > > > > > > > >
> > > > > > > > > any views?
> > > > > > > > >
> > > > > > > > > thx!
> > > > > > > > > cherif
> > > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > 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
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > >
> > > > > >
> > > >
> > -----------------------------------------------------------------------------------------
> > > > > > > Cherif P. Sahyoun
> > > > HST-MEMP
> > > > > > >
> > > > > > > Developmental Neuroimaging of Cognitive Functions
> > > > > > >
> > > > > > > C: 617 688 8048
> > > > > > > H: 617 424 6956
> > > > > > > [log in to unmask]
> > > > > > >
> > > > > > > "Live as if this were your last day. Learn as if you'll live
> > > > forever"
> > > > > > > Ghandi
> > > > > > >
> > > > > >
> > > >
> > -------------------------------------------------------------------------------------------
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > >
> > > >
> > -----------------------------------------------------------------------------------------
> > > > > Cherif P. Sahyoun
> > HST-MEMP
> > > > >
> > > > > Developmental Neuroimaging of Cognitive Functions
> > > > >
> > > > > C: 617 688 8048
> > > > > H: 617 424 6956
> > > > > [log in to unmask]
> > > > >
> > > > > "Live as if this were your last day. Learn as if you'll live
> > forever"
> > > > > Ghandi
> > > > >
> > > >
> > -------------------------------------------------------------------------------------------
> > > > >
> > > >
> > > > --
> > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > >
> > -----------------------------------------------------------------------------------------
> > > Cherif P. Sahyoun HST-MEMP
> > >
> > > Developmental Neuroimaging of Cognitive Functions
> > >
> > > C: 617 688 8048
> > > H: 617 424 6956
> > > [log in to unmask]
> > >
> > > "Live as if this were your last day. Learn as if you'll live forever"
> > > Ghandi
> > >
> > -------------------------------------------------------------------------------------------
> > >
> >
> > --
> > 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
> >
>
>
>
> --
> -----------------------------------------------------------------------------------------
> Cherif P. Sahyoun HST-MEMP
>
> Developmental Neuroimaging of Cognitive Functions
>
> C: 617 688 8048
> H: 617 424 6956
> [log in to unmask]
>
> "Live as if this were your last day. Learn as if you'll live forever"
> Ghandi
> -------------------------------------------------------------------------------------------
>
--
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
|