Yes
On 01/13/2017 03:28 PM, John Anderson wrote: > Thank you Doug for the advice , > I will follow your pipeline, I see that the command "gtmseg " is part > of Freesurfer 6. Can I apply it on recons generated by Freesurfer 5.3 ? > Best, > John > *Sent:* Friday, January 13, 2017 at 3:16 PM > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > These differences are hard to track down because they are so subtle. > > You may want to use our PET module, which includes PVC > > http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer > > > On 01/13/2017 03:10 PM, John Anderson wrote: > > I am working on surface-based analysis to study the differnce in PET > > signal in the cortex between two groups. > > 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". How can I check that this differnce is a real differnce and > > not related to partial volume effect? > > Best, > > John > > *Sent:* Friday, January 13, 2017 at 2:46 PM > > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > What is the modality you are looking at? > > > > > > On 01/13/2017 02:08 PM, John Anderson wrote: > > > Thank you very much Doug, > > > Kindly, do you suggest me any steps to avoid patial volume effects in > > > surface based analyses ? > > > Best, > > > John > > > *Sent:* Friday, January 13, 2017 at 12:21 PM > > > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > > > *To:* freesurfer@nmr.mgh.harvard.edu > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac) > > > > > > > > > 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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://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 > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 > <http://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 > <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
