It looks like mri_convert cannot find information about the orientation of the volume. The analyze format does not have fields in the header for this information, but SPM usually adds a .mat file. It does not look like fs_sub.img has a fs_sub.mat, so mri_convert is guessing (incorrectly) what the direction cosines are.
You can fix this in multiple ways: (1) get the proper .mat file (2) get a new copy of mri_convert from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer, and re-run mri_convert specifying the direction cosines on the command-line using the --in_X_direction, where X is i, j, or k corresponding to col, row, and slice doug Felix Blankenburg wrote: > > Dear Bruce, Doug and Xiangchuan and others, > > First of all thank you very much for your help. The processing of the > surfaces works now very well. But I got a few problems with the overlay of > the SPM99 results. After conversion of the 'analyze' data (t-maps and epis) > with mri_convert the bshort and bfloat images looked very warped. It seems > that the program is not able to compute the correct dimensions i. e. does > not read the header information's. After making a functional directory, > creating the analyse.dat, register.dat in the image subdirectory and the SPM > t-map (changing the write filtered to float type) it seems that the > conversion of the functional data leads to the described problem. Enclosed > is the log-file for the conversion of the data: > > mri_convert fs_sub.img sub --out_type bfloat > > reading from fs_sub.img... > > INFO: analyzeRead(): found 1 files for fs_sub.img > > INFO: analyzeRead(): min = 0, max = 4.3109 > > 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, 1, 1) > > j_ras = (0, 0.5, 0) > > k_ras = (0, 0, 0.5) > > warning: output volume axes are not orthogonal > > i_ras = (1, 1, 1) > > j_ras = (0, 0.5, 0) > > k_ras = (0, 0, 0.5) > > writing to sub... > > INFO: bvolumeWrite: stem = sub > > Does anyone know the problem and have a solution for this or could help me > with a step to step documentation how to overlay SPM results onto the brain > surfaces. Thank you very much in advance, > > Felix > > Dr. med. Felix Blankenburg > Dept. of Neurology > Charité, Humboldt-University > Schumannstr. 20/21 > 10117 Berlin, Germany > > Phone: ++49-30-450 560 194 > Fax: ++49-30-450 560 952 > http://www.charite.de/ch/neuro/forschung/teams/klinisch/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
