Hi,

Q1:
I am using Dimon and then running the script created by Dimon to reconstruct a Sagittal mprage collected on a siemens 3T system. The images looks fine but when I try to cross check the co-ordinates between the raw dicom images and the reconstructed afni image they do not match. [I am comparing the tag (0020,0032) of the first raw dicom image with the afni coods for the upper left corner of the first sag slice i.e Sag viewer set to the 0th slice, Axial set to the last slice and Coronal set to the 0th slice]

Am I doing/checking something in a wrong way?

Commands:
Dimon -dicom_org -infile_prefix \"*\" -GERT_Reco -quit
GERT_Reco script
#!/bin/tcsh

# This script was automatically generated by \'Dimon\'.
#
# Please modify the following options for your own evil uses.

set OutlierCheck = \'\' # use \'-skip_outliers\' to skip
set OutPrefix = \'OutBrick\' # prefix for datasets


to3d -prefix ${OutPrefix}_run_006 \\
-time:zt 160 1 2.02sec alt+z \\
-@ < dimon.files.run.006

Q2.
I used the same commands as above on another Sagittal mprage collected at a 1.5T siemens and the check between the raw dicom first slice matched with the afni co-ods for the last Sagittal slice [Sag viewer set to the last slice, Axial set to the last slice, coronal set to the 0th slice]

I am assuming this is the case because images to collected R to L instead of L to R. Am I thinking correctly?

PS: this does not seem to be an issue for the GE images as the co-ods (tag 0020,0032) first slice of the raw dicom matches with the afni coods for the first sagittal slice (Sag viewer set to the 0th slice, Axial last slice, Coronal 0th slice)

Please help. Currently very confused!!

Thanks a lot,
aparna