On 12/18/2013 12:08 PM, Hamza Alshuft wrote: > > Dear Freesurfer experts > > > When I ran: mris_anatomical_stats -i 0 0.002 -l label/lh.roi.label -t > / surf/lh.MD.mgh -b -f stats/lh.roi.stats subid lh to get the DTI > value for a particular label, the function does not really take the > thresholds I set into account as it displayed: > > only considering thicknesses in the range [0.0,0.0]. > You can ignore this. It is just a display error in that it only prints out 1 digit past the decimal, so the upper limit gets rounded to 0.0, but internally it will use 0.0 and 0.002. > > Is it because the range I want to detect is too small? > > Also, the result is always 0.001(mean DTI) +/-0.000 (std) for all the > subjects and all the different labels. >
This is also probably a rounding/precision error in the output. I might use a combination of mri_binarize and mri_segstats for this. Eg, mri_binarize --i lh.MD.mgh --min 0 --max .002 --o lh.MD.mask.mgh mri_segstats --mask lh.MD.mask.mgh --slabel subject lh lh.roi.label --id 1 --sum lh.roi.stats See if that gives you better results. If the precision of the digits in lh.roi.stats is not good enough, you can add --mul 100 to multiply everything by 100. doug > Thank you very much! > > Lily > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please send it back to me, and immediately delete > it. Please do not use, copy or disclose the information contained in > this message or in any attachment. Any views or opinions expressed by > the author of this email do not necessarily reflect the views of the > University of Nottingham. > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses which could damage your > computer system, you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > > > > > _______________________________________________ > 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.