yes, I think that was the issue and it is now sorted out Bruce On Tue, 4 Aug 2015, Douglas N Greve wrote:
> 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
