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
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)
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>
> > > 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
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>
> > > 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
_______________________________________________ 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.
