[MINC-users] Volume orientation problem

[EJ Nikelski]

Dear List,

   I should probably be able to figure this out myself, but I'm stumped.
In short, I have a DICOM format T1 volume which I convert to minc using
dcm2mnc, and then transform into Talairach space. Conversion to minc
looks terrific when viewed in Display, but the Talairach space volume
looks *very* wrong.

Here are the details:

(1) DICOM volume produced from a GE Signa Excite 3T scanner. Conversion
to minc produces a volume that looks like this ...

>>>>>>
 jnikelski at Brunnhilde:~/tmp/xxx$ mincinfo anat_stephane.mnc
file: anat_stephane.mnc
image: signed__ short -32768 to 32767
image dimensions: yspace zspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    yspace                    248    -0.800001     -72.2295
    zspace                    512    -0.371094      110.619
    xspace                    512    -0.371094      90.7169
<<<<<<<

(2) Run mritotal/mincresample. mritotal provides an initial/final
objective function of 0.1900/0.1897 (not good?) The xfm is ...

>>>>>>>
jnikelski at Brunnhilde:~/tmp/xxx$ cat anat_stephane.xfm
MNI Transform File
%Fri Sep 16 12:34:42 2005>>> /usr/local/bin/minctracc
/var/tmp/mritotal_1964//anat_stephane_8_dxyz.mnc
/usr/local/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
anat_stephane.xfm -transformation
/var/tmp/mritotal_1964//anat_stephane_8tmp2c.xfm -lsq9 -xcorr
-model_mask /usr/local/bin/../share/mni_autoreg/average_305_8_mask.mnc
-center -2.655523 -169.076736 9.518312 -step 4 4 4 -tol 0.004 -simplex 2
%(Package mni_autoreg 0.98u, compiled by jnikelski at Brunnhilde
(i686-pc-linux-gnu) on Mon Sep 12 16:07:47 EDT 2005)

Transform_Type = Linear;
Linear_Transform =
 1.10752904415131 -0.0873657912015915 0.0189949013292789 -12.5382280349731
 0.0655834898352623 0.592145144939423 -1.10042119026184 95.9860992431641
 0.0736042037606239 1.05778276920319 0.573587834835052 155.421844482422;
<<<<<<<<

(3) When I pull up the Talairach volume in Display I get ...

    (a) The sagittal image, which was pointing to the left, has been
rotated 90 degrees counter-clockwise and is pointing down ... and is
clipped.
    (b) The coronal view now looks kind of axial ... and is clipped.
    (c) The axial view now looks coronal, and is upside-down.


Help? I'm sure that this must be due to the initial orientation info fed
to dcm2mnc being incorrect ... but I have no idea how to feed this
process orientation information.

Cheers,

-Jim