On 01/12/2017 05:20 PM, John Anderson wrote: > Thank you very much Doug and thank you for briniging the issue of > "partial volume effect " to my attention. Kindly, I have one last > question. > I found in wiki that the default values for projfrc value are between > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, > 2 ", In other words, less than zero means the surface based analysis > is running at a lower level of the white matter. Yes > Can the issue of the partial volume effect be avoided by using larger > numbers for "projfrac" ? No, PVEs can't be avoided that way. > Bests, > John > *Sent:* Thursday, January 12, 2017 at 5:08 PM > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > yes, that is correct. However, understand that there might only be a > difference of 1mm between those two locations, so it could easily be a > partial volume effect > > > On 01/11/2017 08:50 AM, John Anderson wrote: > > Thank you Doug, > > Exactly! I meant GM near the CC. > > When I used "projfrac=0.5 " there was no differnce between the groups > > at "cwp 0.05", and when I changed the "projfrac to 0" I got > > significant differnce between the groups in specific areas at "cwp > > 0.01". Kindly, how can this be explained? I highly appreciate if you > > help me to understand this point: > > For "projfrac =0" I expect the surface based analysis to > > be running close to white matter. Right? and when I used > > "projfrac=0.5" the analysis is running in the middle area between pial > > and white. When the analysis is not showing any differne between the > > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that > > means the differnce between the groups is deeper and closer to white > > matter. Is this correct? > > Thank you for any input and clarification! > > Bests, > > John > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM > > *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu> > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > > > When you say in the corpus callosum, do you mean in WM? The > > surface-based analysis is only for cortical GM. If you mean in GM near > > the CC, then the analysis is appropriate. The projfrac parameter sets > > the sampling location between the white and pial surfaces where 0.5 > > means half way. > > > > On 1/10/17 8:07 AM, John Anderson wrote: > > > > Dear FS experts, > > I am working on surface based analysis using freesurfer. I want to > > inquire about the flag "projfrac" in the command "mris_preproc" > > I ran voxel wise analysis including the same subjects. I found > > differnce between the groups in areas close to the corpus > > callosum. I want to get the same results using surface based > > analysis. If I use the projfrac=0.5 is this able to show the same > > results that I got in voxel wise analysis at the level of the > > corpus callosum. Do I need to use differnt number for projfrac ? > > Thank you for any advice. > > > > Best, > > John > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ 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. > > > > > > _______________________________________________ > > 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 > <http://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 > > > _______________________________________________ > 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