Hi Sam, it sounds like what you are doing is correct. Another possible solution would be to use mri_binarize, something like mri_binarize EXAMPLE.nii.gz --match 17 --o left.hippo.nii.gz This matches the number rather than doing a thresholding. It seems like the thresholding should work, but there might be some issue internal to fslmaths that is not handling the numerical precision correctly. doug
On 08/16/2012 09:51 PM, Sam Carpenter wrote: > Dear life savers, headache relievers and brain science dreamers, > > PROLOG: > I'm trying to separate out some regions from a .nii.gz file. I start with > a surface parcellation in .annot (Freesurfer land) that I convert to > EXAMPLE.nii.gz using mri_aparc2aseg. > > THE GOAL: To get a .nii.gz file for each one of these regions. Using > fslmaths, I threshold the EXAMPLE.nii.gz file above& below the intensity > of that region& save as REGION_name.nii.gz. > > THE PROBLEM: This method is working for the majority of the regions. But > many of the output REGION_name.nii.gz files are completely empty. They are > there in the original EXAMPLE.nii.gz but are lost in the thresholding > some(how/where). > > THE SOLUTION: Your kind reply... > > > Thanks very much. > -Sam > > > _______________________________________________ > 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.
