I've given it a try in which I do not include "* --out_orientation RAS" *for writting an nii file (see output below). In doing so the new aseg.nii file appears to be the exact same as the original nii files I created (i.e. the number of voxels for a given segmentation ID did not change between the old and new nii file and neither of these are matching the stats file). Do you have another suggestion for fixing this? I ask because some of the smaller structures can have up to a 30% change in the number of voxels representing a given structure (comparing the nii file to the stats file).
r500711$ mri_convert aseg.mgz aseg.nii mri_convert aseg.mgz aseg.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to aseg.nii... On Fri, Jul 31, 2015 at 2:31 PM, Jonathan Plasencia <jplas...@asu.edu> wrote: > Ok, I will give this a look. Thank you everyone. > Best, > > Jon > > >> cheers >> Bruce >> >> On Fri, 31 Jul 2015, Jonathan Plasencia wrote: >> >> This is what we did from terminal: >>> >>> mri_convert aseg.mgz aseg.nii --out_orientation RAS >>> mri_convert aseg.mgz aseg.nii --out_orientation RAS >>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>> reading from aseg.mgz... >>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>> i_ras = (-1, 0, 0) >>> j_ras = (0, 0, -1) >>> k_ras = (0, 1, 0) >>> Setting output orientation to RAS >>> Reslicing using trilinear interpolation >>> writing to aseg.nii... >>> >>> ** I ran this command from within the subject's mri folder. >>> >>> Should we try this without --out_orientation RAS ? >>> >>> Best, >>> >>> Jonathan Plasencia >>> Graduate Student >>> NSF Graduate Research Fellow >>> School of Biological and Health Systems Engineering >>> Arizona State University >>> Email: jplas...@asu.edu >>> Phone: (480)861-7017 >>> >>> On Fri, Jul 31, 2015 at 12:54 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> >>> wrote: >>> why are you specifying the output orientation? That is probably >>> causing >>> resampling >>> >>> On Fri, 31 Jul 2015, >>> Jonathan Plasencia wrote: >>> >>> > >>> > We are using the following line: >>> > >>> > >>> > mri_convert aseg.mgz aseg.nii --out_orientation RAS >>> > >>> > >>> > >>> > Best, >>> > >>> > Jonathan Plasencia >>> > Graduate Student >>> > NSF Graduate Research Fellow >>> > School of Biological and Health Systems Engineering >>> > Arizona State University >>> > Email: jplas...@asu.edu >>> > Phone: (480)861-7017 >>> > >>> > On Fri, Jul 31, 2015 at 12:31 PM, Lilla Zollei >>> <lzol...@nmr.mgh.harvard.edu> >>> > wrote: >>> > >>> > Hi Jon, >>> > >>> > What is the exact command that you used for the below >>> described >>> > conversion? >>> > >>> > Lilla >>> > >>> > On Fri, 31 Jul 2015, Jonathan Plasencia wrote: >>> > >>> > > I've converted the aseg.mgz file to .nii (need data in >>> nii to >>> > do some further work on the data). However, the number >>> of voxels >>> > for a given structure changes when comparing the stats >>> file >>> > (from freesurfer) to the created .nii file. What is >>> happening >>> > here? Is there a fix for this? I would expect the number >>> of >>> > > voxels for a given structure should be the same >>> between the >>> > stats file and the .nii file. >>> > > Note: I get the voxel values in the stats file from >>> the >>> > NVoxels column. I get the voxel values in the generated >>> .nii >>> > file by using matlab to count the number pixels with a >>> given >>> > SegId value (i.e. given intensity value). >>> > > >>> > > >>> > > Best, >>> > > >>> > > Jon >>> > > >>> > > >>> > _______________________________________________ >>> > 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. >>> > >>> > >>> > >>> > >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >> _______________________________________________ >> 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. >> >> >
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