Re: [Freesurfer] surface based analysis (projfrac)
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 corr
Re: [Freesurfer] surface based analysis (projfrac)
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 > > >
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
Re: [Freesurfer] surface based analysis (projfrac)
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 n
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
Re: [Freesurfer] surface based analysis (projfrac)
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@
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.h
Re: [Freesurfer] surface based analysis (projfrac)
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 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 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.
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
Re: [Freesurfer] surface based analysis (projfrac)
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 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.
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.
