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
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" greve@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
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" greve@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" greve@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 greve@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
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" greve@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" greve@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" greve@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 greve@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 greve@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
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" greve@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" greve@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" greve@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" greve@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 greve@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 greve@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 greve@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
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" greve@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" greve@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" greve@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" greve@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" greve@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 greve@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 greve@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 greve@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 greve@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
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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John Anderson