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; > -------------------- > *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 > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
