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. Can the issue of the partial volume effect be avoided by using larger numbers for "projfrac" ?
Bests,
John
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)
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
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
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
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.
