yes On Wed, 30 Nov 2011, Joshua Lee wrote:
Actually, I have one last-last question. If I use mri_binarize on my aseg.mgz file, does it remain in the same 'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz, will that z -coordinate still be valid in nifti file i'd have mri-Binarize create?Josh On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee <jki...@ucdavis.edu> wrote: I'm glad you caught that because I suddenly got really confused! Thank Bruce for all your hard work! Josh - On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: oops, I meant the aseg.stats, not the aseg.mgz On Wed, 30 Nov 2011, Joshua Lee wrote: Hi Bruce, I'll see if I can phrase this right In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp??? Josh On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: probably not, as the aseg.stats calculation uses partial volume estimates. cheers Bruce On Wed, 30 Nov 2011, Joshua Lee wrote: Hey Doug, THanks. That looks simpler. I'll probably use that. Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats? Josh On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/FreeSurferColorLUT.txt doug Joshua Lee wrote: Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh ------------------------------------------------------------------------ _______________________________________________ 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 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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