There is currently not a way to mask for anything but the brain. I just found out that that did not work (and never had). That has been fixed. I also added the ability to specify an FDR mask using an environment variable, like
setenv TKM_FDR_MASK yourfdrmask.mgz This will look in the $SUBJECTS_DIR for subject/mri/yourfdrmask.mgz. Note that you must check the "mask to brain" option next to the FDR button. This two changes will be live in both dev and stable upon the next update. You can make the mask you want from aparc+aseg.mgz using mri_binarize with the --match option to choose the structures you want to include in the mask. doug Yigal Agam wrote: > Hi, > > Is it possible to restrict FDR correction to gray matter in tkmedit? > > Thanks > _______________________________________________ > 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.
