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 >
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