Hi Al,
I've replicated the problem and am working on a fix. doug > The resulting "orig" image, when viewed in MEDIT, is flipped: Albert Kim wrote: > > Dear all, > > I'm having trouble with the use of mri_convert to convert my SPM/Analyse > structural volume to COR format. > (mri_convert foo.img /Subjects/E12246/mri/orig/) > The resulting "orig" image, when viewed in MEDIT, is flipped: > the second volume index increases from posterior to anterior > the third volume index increases from inferior to superior > (i'm not sure whether the first index is flipped, bcs it is > left-right) > > This problem does not occur when I use "Setup Structural Scan > Parameters" from the GUI to read the iamge, and then CONVERT/AVERAGE. > > Does anybody know if there is a problem here? > > Here is a copy of the output from mri_convert > > mri_convert Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img >Subjects/E12246C/mri/orig/ > # mri_convert Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img >Subjects/E12246C/mri/orig/ > mri_convert > Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img > Subjects/E12246C/mri/orig/ > reading from > Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img... > INFO: analyzeRead(): found 1 files for > Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img > INFO: analyzeRead(): min = 0, max = 258 > TR=0.00, te=0.00, flip angle=0.00 > warning: volume may be incorrectly oriented > warning: input volume axes are not orthogonal > i_ras = (1, 0.613839, 0.613839) > j_ras = (0, 0, 1.16364) > k_ras = (0, 1.16364, 0) > changing data type... > reslicing (interpolate)... > writing to Subjects/E12246C/mri/orig/... > > Thanks > Al Kim > Department of Psychology > University of Washington, Box 351525 > Seattle, WA. 98195, USA > E-Mail: [EMAIL PROTECTED]; Tel: (206)543-2395 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
