I did run a registration (no initial structural image, only a main
structural image (with skull removed)). I had preprocessed the data (but
not registered) in a separate run and used the resulting
filtered_func_data from that as the input file for my data analysis.
Do you happen to have a small sample data set where you know that it'll
work? Something from the feeds-directory maybe? With that I could check
whether Featquery works in general on my machine.
Kerstin.
--
WW
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Life is too short: CARPE DIEM
On Tue, 27 Jul 2004, Stephen Smith wrote:
> Quick question - did you maybe not run registration on this FEAT run?
> Looking at the featquery code, it seems like there might be a buglet -
> that it is unhappy if you haven't run registration (which _should_ be
> unnecessary if you are using a mask in the native space of the lowres fmri
> data).
>
> If this is the case I'll send you a patch for this.
>
> Cheers.
>
>
> On Mon, 26 Jul 2004, Kerstin Preuschoff wrote:
>
> > The problem remains unsolved - at least for me. I've attached the
> > report.txt file (report.log is empty) as well as the avwhd output for
> > the three files that I am trying to use. As far as I can tell the
> > dimensions match, i.e. dim1-3. Am I missing something?
> >
> > Thanks,
> > Kerstin.
> >
> > > Hi - the number of KB an image is isn't normally very useful, as
> > > different images may be of different datatypes (int, 16bit int,
> > float etc)
> > > so really you need to check these size issues using "avwhd" to check
> > image
> > > matrix dimensions.
> > >
> > > Hope this helps! Steve.
> > >
> > >
> > > On Mon, 21 Jun 2004, Anda van Stegeren wrote:
> > >
> > > > Hi,
> > > > I checked the dimensions of the mask. It is in standard space.
> > > > I used the same mask on an other PC, where it worked out fine in
> > Featquery.
> > > > I can open the mask in MRICro as well, so i really don't have a
> > clue what to do next.
> > > >
> > > > The only weird thing that stroke me, but might as well have
> > nothing to do with it, is that in the .gfeat directory there is a
> > bg_image.hdr and a mask.hdr that are both 882 kB in size,
> > > > whereas the 'EXPmask' I want to use, which i drew in FSLview, is
> > 1.763 kB.
> > > >
> > > > And when I enter a coordinate in Featquery (with the EXPmask
> > entered as 'mask') it a mask of 3526 kB (so double the size of my
> > original mask) that is saved in the "Featquery directory" next to the
> > log text "Error - mask size doesn't match any of the images in the
> > FEAT directory".
> > > >
> > > > Thats about all I can tell. Any help is greatly appreciated...
> > > >
> > > > Drs. Anda van Stegeren,
> > > > University of Amsterdam
> > > > Department of Clinical Psychology
> > > > Roetersstraat 15
> > > > 1018 WB Amsterdam
> > > > The Netherlands
> > > > tel. ++ 31 20 525 6799
> > > > fax. ++31 20 639 1369
> > > > E-mail: [log in to unmask]
> > > >
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]On
> > > > Behalf Of Tim Behrens
> > > > Sent: maandag 21 juni 2004 12:23
> > > > To: [log in to unmask]
> > > > Subject: Re: [FSL] Featquery question
> > > >
> > > >
> > > > Hi there -
> > > >
> > > > When you specify a mask for featquery it tries to identify
> > > > which space you have drawn the mask in by examining the dimensions
> > of
> > > > the mask. I believe the three images it compares with are:
> > > >
> > > > example_func
> > > > highres
> > > > standard
> > > >
> > > > (pls correct me if someone knows better)
> > > >
> > > > If your mask dimensions do not match the dimensions of any of
> > these three
> > > > images
> > > > then featquery does not know which transform to apply to your mask
> > before
> > > > interrogating the filtered_func_data.
> > > >
> > > > I guess you should check the image dimensions of your mask against
> > those
> > > > of the space in which you are drawing.
> > > >
> > > > Hope this is clear
> > > >
> > > > Tim
> > > >
> > > > -------------------------------------------------------------------
> > ------------
> > > > Tim Behrens
> > > > Centre for Functional MRI of the Brain
> > > > The John Radcliffe Hospital
> > > > Headley Way Oxford OX3 9DU
> > > > Oxford University
> > > > Work 01865 222782
> > > > Mobile 07980 884537
> > > > -------------------------------------------------------------------
> > ------------
> > > >
> > > > On Sat, 19 Jun 2004, Anda van Stegeren wrote:
> > > >
> > > > > Hi,
> > > > > Since I was confronted with exactly the same message as Kerstin
> > Preuschoff I mailed her. She hadnt been able to send the requested
> > files, but asked me to send mine..
> > > > >
> > > > > 1) the report.log file = empty
> > > > > 2) the report.txt file says:
> > > > >
> > > > > Processing FEAT directory 1 :
> > C:/cygwin/data/anda/HLA.gfeat/cope1.feat
> > > > > Error - mask size doesn't match any of the images in the FEAT
> > directory
> > > > >
> > > > > any idea ?
> > > > > best regards,
> > > > > Anda van Stegeren
> > > > >
> > > > > Drs. Anda van Stegeren,
> > > > > University of Amsterdam
> > > > > Department of Clinical Psychology
> > > > > Roetersstraat 15
> > > > > 1018 WB Amsterdam
> > > > > The Netherlands
> > > > > tel. ++ 31 20 525 6799
> > > > > fax. ++31 20 639 1369
> > > > > E-mail: [log in to unmask]
> > > > >
> > > > >
> > > > > ________________________________
> > > > >
> > > > > Van: FSL - FMRIB's Software Library namens Stephen Smith
> > > > > Verzonden: vr 4-6-2004 4:48
> > > > > Aan: [log in to unmask]
> > > > > Onderwerp: Re: [FSL] Featquery question
> > > > >
> > > > >
> > > > >
> > > > > Hi - could you send in the report.txt and report.log files for
> > us to look
> > > > > at - thanks.
> > > > >
> > > > >
> > > > > On Thu, 3 Jun 2004, Kerstin Preuschoff wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > when trying to run featquery I get the following message in
> > report.txt
> > > > > >
> > > > > > Error - mask size doesn't match any of the images in the FEAT
> > directory
> > > > > >
> > > > > >
> > > > > > As a check I took the mask.hdr from the feat-directory itself.
> > That should
> > > > > > definitely have the correct image size, right? But I still get
> > the same
> > > > > > error message. I also checked the headers for the dim1-3 which
> > all
> > > > > > matched. Are there any other constraints for the mask image
> > size that I
> > > > > > am not aware of? Is there a min/max number of voxels in the
> > mask?
> > > > > >
> > > > > > Thanks,
> > > > > > Kerstin.
> > > > > >
> > > > > > --
> > > > > >
> > > > > >
> > > > > > WW
> > > > > > /__\
> > > > > > | oo | _WWWWW_
> > > > > > (|_()_|) / o o \
> > > > > > \__/ (| __O__ |)
> > > > > > /|\/|\ \ \___/ /
> > > > > > |||||||| /-------\
> > > > > > |||||||| |=========|
> > > > > > |||||||| |=========|
> > > > > > #################################
> > > > > > Life is too short: CARPE DIEM
> > > > > >
> > > > > >
> > > > > > Kerstin Preuschoff
> > > > > > 139-74
> > > > > > California Institute of Technology
> > > > > > Pasadena, CA 91125
> > > > > >
> > > > >
> > > > > 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
> > > > >
> > > >
> > >
> > > 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
> > >
> > >
> >
> >
> >
> >
>
> 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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