[MINC-users] nii2mnc problem

[EJ Nikelski]

Hi all,

   Thanks Andrew.  I placed a couple of samples into
"/data/scratch/scratch1/jim/nifti".  There you will find volumes for 2
subjects: (1) subject 0002, who is reflective of most of my subjects,
and (2) subject 0008, who, following conversion using the same input
params as used for S0002, is upside-down (according to Display).  I
used the following to convert:

nii2mnc -xyz -flipz -flipx 0002-M-NC.nii

   Yup, removing the '-flipz' would likely solve my problem for S0008,
but would likely mess everyone else up.  Just for fun, I ran these
volumes through the LONI debabeler (results are in the 'debabel'
subdir), which appears to have converted them both to minc, without
the need to enter any parameters at all -- suggesting that the nifti-1
meta-data is sufficient to perform the conversion correctly.

Thanks for the help, and pls let me know if you require anything else.

-Jim



On Sun, Apr 20, 2008 at 10:36 AM, Andrew Janke <a.janke at gmail.com> wrote:
> >  I've run into what appears to be a problem with nii2mnc.  I've run a
>  >  few hundred ADNI volumes (nifti-1) through nii2mnc, and after
>  >  determining the proper -flip parameters, all seemed OK ... except,
>  >  that a few volumes, using the same input parameters, were flipped
>  >  along the inferior-superior axis (i.e., the brains were upside-down).
>  >  Now, the problem does not lie with the volume meta-data, as any number
>  >  of other nifti-1 viewers are able to display the volumes normally ...
>  >  only nii2mnc has problems.  I have a samples of both "good" and
>  >  "upside-down" volumes, if anyone wants to take a look.
>
>  Hi Jim,
>
>  Sounds "interesting".  Can you put these recalcitrant volumes up
>  somewhere that I can get at them?
>
>  Thanks
>
>
>  a
>  _______________________________________________
>  MINC-users at bic.mni.mcgill.ca
>  http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University
Tel: (514) 340-8222 x 2298
Fax: (514) 340-8295