Hi freesurfer programmers, I have a specific question reagrding the output of mri_label2vol. The image is correctly converted, however the analyze header file has an orientation value set to -1. This is invalid as analyze orient fields can only be 0-5, and my next scripts rely on the orient string to perform transformations. See - http://eeg.sourceforge.net/mri_orientation_notes.html
Should I manually edit the orient field in the header? or does -1 field = analyze 4? Thanks, Mario Ortega Here is my specific command line output. running the command: *mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg. img --regheader aparc+aseg.mgz* /mnt/data/freesurfer Number of labels: 0 Annot File: (null) Template Volume: rawavg.mgz Outut Volume: aseg-in-rawavg.img Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.25.2.4 2009/07/08 16:28:40 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 88.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Computing registration based on header RegMat: -------- 0.019 0.998 -0.052 0.000; -0.999 0.021 0.035 0.000; 0.036 0.052 0.998 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.019 -0.998 0.052 128.000; -0.036 -0.052 -0.998 128.000; -0.999 0.021 0.035 88.000; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 342870 (46013 filled) ASeg2Vol: done Analyze Output Matrix -0.019 -0.036 -0.999 98.696; -0.998 -0.052 0.021 164.924; 0.052 -0.998 0.035 115.862; 0.000 0.000 0.000 1.000; -------------------- *INFO: set hdr.hist.orient to -1* /mnt/data/freesurfer Number of labels: 0 Annot File: (null) Template Volume: rawavg.mgz Outut Volume: aseg-in-rawavg.img Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0
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