Hi all,
I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial.
But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right?
My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue.
I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?).
I' not sure of which approach to follow now... Does it depend on the measure I'll be using?
Thank you!
Andreia
Hi Andreia
the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than the actual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce
On Fri, 22 Mar 2013, _andreia_@sapo.pt wrote:
Hi all,
I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial.
But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right?
My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue.
I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?).
I' not sure of which approach to follow now... Does it depend on the measure I'll be using?
Thank you!
Andreia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thank you for the quick response!
In the meanwhile, does that also apply to cortical thickness and volume?
Thank you!
Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia
the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than the actual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce
On Fri, 22 Mar 2013, _andreia_@sapo.pt wrote:
Hi all,
I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial.
But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right?
My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue.
I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?).
I' not sure of which approach to follow now... Does it depend on the measure I'll be using?
Thank you!
Andreia
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.
yes. Surface area will be the affected much more than thickness (and volume of course scales with area)
On Fri, 22 Mar 2013, _andreia_@sapo.pt wrote:
Hi Bruce,
Thank you for the quick response!
In the meanwhile, does that also apply to cortical thickness and volume?
Thank you!
Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia
the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than the actual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce
On Fri, 22 Mar 2013, _andreia_@sapo.pt wrote:
Hi all,
I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial.
But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right?
My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue.
I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?).
I' not sure of which approach to follow now... Does it depend on the measure I'll be using?
Thank you!
Andreia
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.
Ok, that was my guess... I am running against a deadline, any news on automatically computing the correct threshold script? Will I be able to use it in 5.0?
Thanks you!
Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
yes. Surface area will be the affected much more than thickness (and volume of course scales with area)
On Fri, 22 Mar 2013, _andreia_@sapo.pt wrote:
Hi Bruce,
Thank you for the quick response!
In the meanwhile, does that also apply to cortical thickness and volume?
Thank you!
Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia
the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than the actual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce
On Fri, 22 Mar 2013, _andreia_@sapo.pt wrote:
Hi all,
I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial.
But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right?
My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue.
I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?).
I' not sure of which approach to follow now... Does it depend on the measure I'll be using?
Thank you!
Andreia
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@nmr.mgh.harvard.edu
-
_andreia_＠sapo.pt -
Bruce Fischl