I don't know about the first step but 2 and 3 look ok. But why are you using the aseg? It will just give you the lh and rh cerebral WM
On 06/30/2014 03:11 PM, Alshikho, Mohamad J. wrote: > > Hi Fs Experts, > > In order to calculate the mean diffusivity MD in my DTI data I did the > following: > > 1.For the Eigvals.nii (the output of dt_recon) I used the following > command line: fslmaths eigvals –div 3 md.nii > > 2.mri_vol2vol –mov md.nii --reg register.dat --fstarg -- interp > nearest -- o md.anat.mgh > > 3.mri_segstats --seg $SUBJECTS_DIR/mri/aseg.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --seg-erode 2 --i md.anat.mgh > --sum md.stats > > is this correct ? > > I highly appreciate any suggestions and advices > > 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.
