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