Hi,

DICOM images from the scanner that are being reconstructed using the to3d program are giving the following warning and the resulting anatomical images have bands. In addition, the orientation of the axial and coronal images is wrong - the orientation is 90 degrees CCW

Moreover, something odd is happening in the GUI (happens sporadically) - pressing coronal button and getting axial slice (in wrong orientation) pop up.

- anatomical images were acquired in the sagittal plane

Fatima s0002:to3d -prefix anat_test1 E*
++ to3d: AFNI version=AFNI_2008_07_18_1710 (Aug 5 2008) [32-bit]
++ Authored by: RW Cox
++ Counting images: total=120 2D slices
++ Each 2D slice is 256 X 256 pixels
++ Voxel dimensions: 0.9375 X 0.9375 X 1.5000 mm
++ Image data type = short
++ Reading images: ........................................
++ to3d WARNING: 57288 negative voxels (0.728455%) were read in images of shorts.
++ It is possible the input images need byte-swapping.
++ 3D dataset written to disk

There was a previous message from 3/12/08 that had a similar problem and it was suggested to modify the .afnirc file. Where can I find this file? I am not finding it in abin.

Thank you,
Liat

PS.
3dinfo
Dataset File: anat_test1+orig
Identifier Code: XYZ_OhJi6z0RNRflgWOciGlf0A Creation Date: Thu Aug 14 12:54:30
2008
Dataset Type: Spoiled GRASS (-spgr)
Byte Order: MSB_FIRST [this CPU native = MSB_FIRST]
Storage Mode: BRIK file
Storage Space: 15728640 (16 million) bytes
Geometry String: "MATRIX(0,0,-1.5,79.5902,0.9375,0,0,-124.414,0,-0.9375,0,113.83
1):256,256,120"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Anterior-to-Posterior
second (y) = Superior-to-Inferior
third (z) = Left-to-Right [-orient ASL]
R-to-L extent: -98.910 [R] -to- 79.590 [L] -step- 1.500 mm [120 voxels]
A-to-P extent: -124.414 [A] -to- 114.648 [P] -step- 0.938 mm [256 voxels]
I-to-S extent: -125.231 -to- 113.831 [S] -step- 0.938 mm [256 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: -32761 to 32761

----- HISTORY -----
[fatima@mac118030.med.cornell.edu: Thu Aug 14 12:54:30 2008] to3d -prefix anat_test1 E006263S0002I00001.DCM E006263S0002I00002.DCM E006263S0002I00003.DCM ... E006263S0002I00119.DCM E006263S0002I00120.DCM