Hi All,
thanks to Al's diligence, I have tracked down a bug in the most recent
version of mri_convert, the one that I mentioned a few weeks ago that
could be downloaded from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer.
There was a problem with the way it was reading the SPM mat file. This
does not apply to older versions, only the one that was on the FTP site
above. I have placed new Linux and SunOS versions at the FTP site with
which you should immediate replace the previous version.
let me know how it goes
doug
Albert Kim wrote:
>
> Dear all,
>
> I'm having trouble with the use of mri_convert to convert my SPM/Analyse
> structural volume to COR format.
> (mri_convert foo.img /Subjects/E12246/mri/orig/)
> The resulting "orig" image, when viewed in MEDIT, is flipped:
> the second volume index increases from posterior to anterior
> the third volume index increases from inferior to superior
> (i'm not sure whether the first index is flipped, bcs it is
> left-right)
>
> This problem does not occur when I use "Setup Structural Scan
> Parameters" from the GUI to read the iamge, and then CONVERT/AVERAGE.
>
> Does anybody know if there is a problem here?
>
> Here is a copy of the output from mri_convert
>
> mri_convert Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img
>Subjects/E12246C/mri/orig/
> # mri_convert Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img
>Subjects/E12246C/mri/orig/
> mri_convert
> Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img
> Subjects/E12246C/mri/orig/
> reading from
> Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img...
> INFO: analyzeRead(): found 1 files for
> Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img
> INFO: analyzeRead(): min = 0, max = 258
> TR=0.00, te=0.00, flip angle=0.00
> warning: volume may be incorrectly oriented
> warning: input volume axes are not orthogonal
> i_ras = (1, 0.613839, 0.613839)
> j_ras = (0, 0, 1.16364)
> k_ras = (0, 1.16364, 0)
> changing data type...
> reslicing (interpolate)...
> writing to Subjects/E12246C/mri/orig/...
>
> Thanks
> Al Kim
> Department of Psychology
> University of Washington, Box 351525
> Seattle, WA. 98195, USA
> E-Mail: [EMAIL PROTECTED]; Tel: (206)543-2395
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422