you can play around with the fill threshold doug
Timothy Vickery wrote: > I see, thanks for the quick clarification. So in the Method 2 there is > a chance that some voxels will show up in multiple ROIs, right? Is > there a modification of Method 2 that maximizes that number of labeled > voxels while ensuring that they will not show up in multiple ROIs? > > Thanks again, > Tim > > > On Fri, Aug 20, 2010 at 4:15 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > The difference is the partial volume correction is different if > there are a bunch of other labels there (aparc+aseg) vs only one label > > doug > > Timothy Vickery wrote: > > Hi all, > > I'm creating binary mask volumes in a subject's native > functional space from the segmented brain in aparc+aseg.mgz > (FS v 4.5). I have found that doing this two different ways > produces different results, and I'm wondering if anyone can > illuminate why this might occur and which method is more > appropriate (or what other method you would suggest)... > > Method 1: Resample aparc+aseg.mgz into native functional space > using > mri_label2vol --seg aparc_aseg.mgz --fillthresh 0.5 [...plus > the rest of the appropriate inputs such as subject's > bold/register.dat] > > Then I just parse the resulting image (using matlab or python > code) into separate binary masks for each unique identifier > that I'm using...E.g., for right IPL I load this image and > create a new volume [newVol = (oldVol==2008)] and save that out. > > Method 2: Create a label file from aparc+aseg.mgz for each > unique identifier that I'm using, and then use mri_label2vol > to produce a binary mask in native functional space: > mri_cor2label --i aparc+aseg.mgz --id 2008 --l rIPL.label > mri_label2vol --label rIPL.label --fillthresh 0.5 [... plus > the rest of the required inputs, same as those used in Method 1] > > Even though these seem like they should be equivalent to me, > and although the masks produced agree for the most part, I > generally get several more voxels per ROI using Method 2 than > I do using Method 1 (and not complete overlap otherwise). For > instance, for one subject, Method 1 yields 308 voxels in rIPL, > but Method 2 yields 316 voxels; disagreement between the two > occurs in a total of 26 of those voxels, so it isn't just a > matter of Method 2 being more generous. The discrepancy seems > to be proportional to the size of the ROI, so I get just a > handful of disagreements for smaller ROIs (but it seems to > happen almost all the time). > Thanks for any advice on which method is better, or a > suggestion of a better method. > > Best, > Tim > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- 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 _______________________________________________ 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.
