Hi,
I tried to find out this from previous contributions but got lost. There's some confusion on which file(s) to use for segmented volumes. FreeSurfer generates the following image and text files: - aseg.mgz - aseg.stats - aparc+aseg.mgz - wmparc.mgz - wmparc.stats
To my best knowledge aseg.stats contains the volumes from the structures in aseg.mgz, but corrected for partial volume effects.
The volumes listed in the aseg.stats and wmparc.stats are in most cases different. Which volumes are the correct ones and to which of the image files are these referring?
Ed
You're right - aseg.stats refers to the aseg.mgz and you should use that. You would only use the wm parcellations from the wmparc.mgz
But what about the labels starting with "lh-ctx-" and "rh_ctx-", like for instance lh-ctx-fusiform (index=1007). In the wmparc.stats file it has a volume of 8249 voxels and in wmparc.mgz 8752 voxels? Is the first pve-corrected and the latter not?
On 18 Jun, 2010, at 13:43, Allison Stevens wrote:
You're right - aseg.stats refers to the aseg.mgz and you should use that. You would only use the wm parcellations from the wmparc.mgz
--
On Fri, 18 Jun 2010, Ed Gronenschild wrote:
Hi,
I tried to find out this from previous contributions but got lost. There's some confusion on which file(s) to use for segmented volumes. FreeSurfer generates the following image and text files:
- aseg.mgz
- aseg.stats
- aparc+aseg.mgz
- wmparc.mgz
- wmparc.stats
To my best knowledge aseg.stats contains the volumes from the structures in aseg.mgz, but corrected for partial volume effects.
The volumes listed in the aseg.stats and wmparc.stats are in most cases different. Which volumes are the correct ones and to which of the image files are these referring?
Ed
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, the difference is partial volume correction. But you should use the values from the ?h.aparc.stats file for cortical parcellations as it uses the more accurate surface-based volumetric calculation.
doug
Ed Gronenschild wrote:
But what about the labels starting with "lh-ctx-" and "rh_ctx-", like for instance lh-ctx-fusiform (index=1007). In the wmparc.stats file it has a volume of 8249 voxels and in wmparc.mgz 8752 voxels? Is the first pve-corrected and the latter not?
On 18 Jun, 2010, at 13:43, Allison Stevens wrote:
You're right - aseg.stats refers to the aseg.mgz and you should use that. You would only use the wm parcellations from the wmparc.mgz
--
On Fri, 18 Jun 2010, Ed Gronenschild wrote:
Hi,
I tried to find out this from previous contributions but got lost. There's some confusion on which file(s) to use for segmented volumes. FreeSurfer generates the following image and text files:
- aseg.mgz
- aseg.stats
- aparc+aseg.mgz
- wmparc.mgz
- wmparc.stats
To my best knowledge aseg.stats contains the volumes from the structures in aseg.mgz, but corrected for partial volume effects.
The volumes listed in the aseg.stats and wmparc.stats are in most cases different. Which volumes are the correct ones and to which of the image files are these referring?
Ed
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
Doug,
I don't understand this since the ?h.aparc.stats file doesn't contain volumes.
Ed
On 18 Jun, 2010, at 15:56, Douglas N Greve wrote:
Yes, the difference is partial volume correction. But you should use the values from the ?h.aparc.stats file for cortical parcellations as it uses the more accurate surface-based volumetric calculation.
doug
Ed Gronenschild wrote:
But what about the labels starting with "lh-ctx-" and "rh_ctx-", like for instance lh-ctx-fusiform (index=1007). In the wmparc.stats file it has a volume of 8249 voxels and in wmparc.mgz 8752 voxels? Is the first pve-corrected and the latter not?
On 18 Jun, 2010, at 13:43, Allison Stevens wrote:
You're right - aseg.stats refers to the aseg.mgz and you should use that. You would only use the wm parcellations from the wmparc.mgz
--
On Fri, 18 Jun 2010, Ed Gronenschild wrote:
Hi,
I tried to find out this from previous contributions but got lost. There's some confusion on which file(s) to use for segmented volumes. FreeSurfer generates the following image and text files:
- aseg.mgz
- aseg.stats
- aparc+aseg.mgz
- wmparc.mgz
- wmparc.stats
To my best knowledge aseg.stats contains the volumes from the structures in aseg.mgz, but corrected for partial volume effects.
The volumes listed in the aseg.stats and wmparc.stats are in most cases different. Which volumes are the correct ones and to which of the image files are these referring?
Ed
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The 4th column is the gray matter volume ("GrayVol").
doug
Ed Gronenschild wrote:
Doug,
I don't understand this since the ?h.aparc.stats file doesn't contain volumes.
Ed
On 18 Jun, 2010, at 15:56, Douglas N Greve wrote:
Yes, the difference is partial volume correction. But you should use the values from the ?h.aparc.stats file for cortical parcellations as it uses the more accurate surface-based volumetric calculation.
doug
Ed Gronenschild wrote:
But what about the labels starting with "lh-ctx-" and "rh_ctx-", like for instance lh-ctx-fusiform (index=1007). In the wmparc.stats file it has a volume of 8249 voxels and in wmparc.mgz 8752 voxels? Is the first pve-corrected and the latter not?
On 18 Jun, 2010, at 13:43, Allison Stevens wrote:
You're right - aseg.stats refers to the aseg.mgz and you should use that. You would only use the wm parcellations from the wmparc.mgz
--
On Fri, 18 Jun 2010, Ed Gronenschild wrote:
Hi,
I tried to find out this from previous contributions but got lost. There's some confusion on which file(s) to use for segmented volumes. FreeSurfer generates the following image and text files:
- aseg.mgz
- aseg.stats
- aparc+aseg.mgz
- wmparc.mgz
- wmparc.stats
To my best knowledge aseg.stats contains the volumes from the structures in aseg.mgz, but corrected for partial volume effects.
The volumes listed in the aseg.stats and wmparc.stats are in most cases different. Which volumes are the correct ones and to which of the image files are these referring?
Ed
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
use aseg.stats for the subcortical volumes. There is a difference between aseg.stats and wmparc.stats for the subcortical volumes because of the partial volume correction.
Ed Gronenschild wrote:
Hi,
I tried to find out this from previous contributions but got lost. There's some confusion on which file(s) to use for segmented volumes. FreeSurfer generates the following image and text files:
- aseg.mgz
- aseg.stats
- aparc+aseg.mgz
- wmparc.mgz
- wmparc.stats
To my best knowledge aseg.stats contains the volumes from the structures in aseg.mgz, but corrected for partial volume effects.
The volumes listed in the aseg.stats and wmparc.stats are in most cases different. Which volumes are the correct ones and to which of the image files are these referring?
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Allison Stevens -
Douglas N Greve -
Ed Gronenschild -
Ed Gronenschild