Hi - I don't think there's anything wrong in the headers. Try the
following:
1. run the swapdim
2. run featregapply <featdir> -f
and check that the upsampled version of the flipped images have appeared
in reg_standard/stats - if so then the higher-level stuff should work
ok...
Cheers, Steve.
On Mon, 9 Jan 2006, Vitaly Napadow wrote:
> hi steve,
>
> unfortunately it was not a space issue.
>
> the problem is due to 8 of the cope inputs being generated by flipping the
> original copes across the midsagittal plane (L hand stim as opposed to
> typical R hand stimulation). i went back and changed 7 of the 8 back to
> the unflipped version, and the error occured at index 67 instead of 60...
> also, i am currently running the whole analysis with unflipped copes and so
> far so good...
>
> so, assuming that the issue is in flipping copes and varcopes, i am not sure
> what i did wrong. i used
>
> avwswapdim input -x y z output
>
> to generate both new copes and varcopes for the 8 scans.
>
> i viewed them and they seem to look as expected (flipped LR)
>
> when i looked at the headers, differences are in pixdim sign and glmax,
> glmin (set to zero once flipped). could either of these changes be causing
> the problem? if so, should i just reformat the headers of all flipped images
> to have the values in the unflipped versions (for example, just rename the
> original headers .hdr files)?
>
> thanks again, headers appear below for unflipped and flipped copes.
> vitaly
>
>
> kharkov:vitaly[286] avwinfo cope_040801mk_015.hdr
> dim1 91
> dim2 109
> dim3 91
> dim4 1
> datatype 16
> pixdim1 2.0000000000
> pixdim2 -2.0000000000
> pixdim3 2.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> glmax 236
> glmin -221
> origin1 46
> origin2 64
> origin3 37
> file_type ANALYZE-7.5
> kharkov:vitaly[287] avwinfo cope_040801mkf_015.hdr
> dim1 91
> dim2 109
> dim3 91
> dim4 1
> datatype 16
> pixdim1 -2.0000000000
> pixdim2 2.0000000000
> pixdim3 2.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> glmax 0
> glmin 0
> origin1 46
> origin2 64
> origin3 37
> file_type ANALYZE-7.5
>
--
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, 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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