Problem:
mri_convert creates a NIFTI image that splits the dual echo, but pads
with empty slices to the full size, e.g. a dual echo of size 256 x
256 with 108 slices will become a 4D volume with 256 x 256 x 108 x 2
instead of 256 x 256 x 54 x 2. The -nth 0 or -nth 1 option will
return a volume of 54 slices, but only half of them with image data
and again the lower half empty.
This does not seem to happen for DICOM.
Does the program look at the "echo number" tag or just de-interleave
based on slice order? I noticed DICOM headers have the echo number
set correctly, but Genesis headers all seem to list all slices as
echo #2. If that's the source of the problem the behavior of
mri_convert is not wrong (since it is getting wrong input), but
unexpected.
In that case: Is there an option to suppress/ignore all echo fields
and read all as one volume?
Environment:
FREESURFER_HOME: /Programs/install/freesurfer
Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1
Kernel info: Darwin 8.11.0 Power Macintosh
Command:
mri_convert -ot nii GE_DualEcho_PD_axial_3mm/I.001 aTestGEDual.nii
Output generated
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from GE_DualEcho_PD_axial_3mm/I.001...
fname_format : GE_DualEcho_PD_axial_3mm/I.%03d
multi-echo genesis file detected (2 echoes)...
TR=3000.00, TE=30.00, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
writing to aTestGEDual.nii...
Many thanks.
Dominik
______________________________________________
DOMINIK MEIER, PH.D.
Center for Neurological Imaging
Brigham & Women's Hospital, Harvard Medical School
221 Longwood Avenue, RF396, Boston, MA 02115
Phone: 617 278-0800
Fax: 617 264-5154
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