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 > 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 _______________________________________________ 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.
