How are you generating the stats? The aseg.stats file uses partial volume correction...
On 08/03/2015 04:48 PM, Jonathan Plasencia wrote: > That is partly correct. The nii is not matching the stats file (which > it is my understanding the stats file is based off the mgz file. If > this is the case then yes to your first question). > > I'll send a mgz file and its stats file directly to your personal > email in a minute: > > fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu> > > Best, > > Jon > > On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > and you are saying that aseg.nii does *not* match the voxel counts > in aseg.mgz? That is surprising. Can you email me the aseg.mgz? > > > On Mon, 3 Aug 2015, Jonathan Plasencia wrote: > > 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 <mailto: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 <mailto:jplas...@asu.edu> > Phone: (480)861-7017 <tel:%28480%29861-7017> > > On Fri, Jul 31, 2015 at 12:54 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu > <mailto: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 > <mailto:jplas...@asu.edu> > > Phone: (480)861-7017 <tel:%28480%29861-7017> > > > > On Fri, Jul 31, 2015 at 12:31 PM, > Lilla Zollei > <lzol...@nmr.mgh.harvard.edu > <mailto: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 > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto: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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
