Use --seg instead of --mask. Also, use --id 1 to get only the ROI in the mask (otherwise it will give you the mask as one ROI and everything outside of the mask as a 2nd ROI)
doug On 02/24/2014 12:51 PM, Garikoitz Lerma-Usabiaga wrote: > Hi, > I have some volume ROIs in diffusion space (1-s and 0-s). I would like > to obtain, for example, the average FA values in that ROI. > > I tried using mri_segstats, but it gives me an error, it needs a > segmentation volume. > mri_segstats --i dmri/dtifit_FA.nii.gz --mask > FSL_waypoint2Hipplh.unc_AS_avg33_mni_bbrlh_headHPC/thres_mask5.nii.gz > --sum fa.stats > > If I substitute --i for --seg I obtain a different error. > > Which command should I use? I tried dmri_pathstats but it is asking > for the file length.samples.txt, which I don't have and don't know how > to generate. > > thanks! > Gari > > > _______________________________________________ > 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.
