That command will work. There's no need to include the mask. Also, I would add --seg-erode 2 which will erode each segmentation by 2 voxel (1mm3) to make sure you avoid partial voluming. That feature might not be available in 5.3, but I can get you a version that does if not doug
On 07/20/2014 01:50 AM, Alshikho, Mohamad J. wrote: > Hi Dear Fs Experts > I will post my question again, hopefully I can find an answer :) > > > In order to calculate the global white matter fractional anisotropy FA > I used (wm.mgz ) the output of recon-all as a mask in the following > command line > > mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --mask wm.mgz --i > fa.anat.mgh --sum fa.stats > > Kindly, Is this correct? > > Thanks > > Mohamad > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
