You should stop using analyze and start using nifti! ... it looks like our code always sets the hdr.orient to -1. I don't know why it does this. In general, we mostly expect that if people care about the actual orientation, then they will use the .mat file that we produce with it. So, I guess just go ahead and change the orientation manually.

doug

Mario Ortega wrote:

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;

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*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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