Re: [Freesurfer] surface based analysis (projfrac)

[John Anderson]

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>
> 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

_______________________________________________
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.