Hi Steve,
That's right, that was exactly it. From a cope2/stats directory I took a
standard-space image (first higher level analysis) and used it as input for
"Pre-threshold Masking" in a second higher level analysis. Closer inspection
of the .hdr file of this image shows a negative voxel-size for pixdim 2 (-2,
see previous attached files). I'm not really sure how to read this, but it
seems quite strange to me. Maybe that's the problem?
Thanks a lot,
Rutger.
-----Original Message-----
From: Stephen Smith [mailto:[log in to unmask]]
Sent: dinsdag 8 april 2003 18:55
To: [log in to unmask]
Subject: Re: [FSL] Problems while masking for main-FX
Hi Rutger,
You're right that the input need to be in the same resolution as the raw
data input to that level. So If I understand you correctly, you put a
standard-space image as input to "Pre-threshold masking" in a higher-level
FEAT run. I just tried this - worked fine for me - is that what you were
doing?
Thanks, Steve.
On Mon, 7 Apr 2003, Goekoop, R. wrote:
>
> Hi,
>
> I've been running a higher-level analysis in FEAT to extract main
> effects on brain activation during task performance (group analysis).
> The resulting contrast was in standard-space and used as a mask for
> pre-threshold masking in a second higher-level analysis (if I
> understand this correctly, FEAT does the analysis first in native
> space, after which the results are transformed to standard-space).
> Here, FEAT reports the following problem:
>
> An exception has been thrown
> Logic error:- detected by Newmat: incompatible dimensions
>
> MatrixType = Rect # Rows = 1; # Cols = 31
> MatrixType = Rect # Rows = 1; # Cols = 31
> MatrixType = Rect # Rows = 2; # Cols = 31
> Trace: MatrixMult; Gsmanager::f_ols_contrast;
> Gsmanager::ols_contrasts; Gsmanager::ols; Gsmanager::initialise;
> Gsmanager::setup.
>
> The analysis then runs on for a while during which this message is
> repeated a couple of times. Then it stops with:
>
> /usr/local/bin/fsl/bin/smoothest -d 44 -m mask -r stats/res4d >
> stats/smoothness Mask and Data (residuals/zstat) volumes MUST be the
> same size!
>
> I suspect the problem might be that my main-FX mask
> (thresh_zstat4.hdr) is in standard space and my Single Subject data
> are all in native space. A quick look at the header-info for the
> relevant files shows different
> voxel-dimensions: single subject 3.28x3.28x6mm, main-FX mask 2x2x1 (see
> attached files). Should I first transform the standard-space mask to
> native-space and then re-run the analysis? Or should a difference in
> voxel-dimensions not matter at all and is there some other problem that
I'm
> not aware off? (And what would be the best way to transform a mask to
native
> space using FSL?).
>
> Any help is greatly appreciated,
>
> Rutger Goekoop.
>
> <<output_hdrinfo_SingleSubject.txt>> <<output_hdrinfo_mask_MFX.txt>>
>
> Drs. R. Goekoop, MD.
> Department of Neurology
> Vrije Universiteit Medical Centre
> P.O. Box 7057, 1007 MB
> Amsterdam, the Netherlands
> Phone: +31 20 444 0316
> E-mail: [log in to unmask] <mailto:[log in to unmask]>
>
>
>
Stephen M. Smith MA DPhil CEng MIEE
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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