Re: [Freesurfer] entorhinal cortex volume question
Hi Folks, I have a question about entorhinal cortex volume. The entorhinal cortex is listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous post on the mailing list, it was mentioned that we should use the volume measurement from ?h.entorhinal_exvivo.stats. We would like to make manual corrections to the entorhinal cortex segmentation (when required). For this task I can create a entorhinal volume from ?h.entorhinal_exvivo.label using mri_label2vol This entorhinal volume will be different from the one in aparc+aseg.mgz My question is: Has anyone published any protocols to somehow combine the two entorhinal volumes ? Or is recommend to take the take the entorhinal volume created from ?h.entorhinal_exvivo.stats. and overlay it on norm.mgz and edit manually (when required). One limitation of this approach is that it would be hard to integrate this entorhinal volume back into aparc+aseg.mgz... Thanks Mehul On Wed, Dec 7, 2011 at 10:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Catherine I guess I would recommend the ex vivo one since it is based explicitly on architecontics and not on guessing locations from folds. cheers Bruce On Wed, 7 Dec 2011, Cat Chong wrote: Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine ___ 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] entorhinal cortex volume question
Hi Mehul the entorhinal label in the aparc was drawn by Rahul based on gyral landmarks. The one in the _exvivo.stats is based on being able to see the layer II islands in ex vivo MRI and hence we believe it is more accurate. Not sure why you need to integrate the ex vivo one back into the aparc+aseg, can you clarify? cheers Bruce On Tue, 29 Jan 2013, Mehul Sampat wrote: Hi Folks, I have a question about entorhinal cortex volume. The entorhinal cortex is listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous post on the mailing list, it was mentioned that we should use the volume measurement from ?h.entorhinal_exvivo.stats. We would like to make manual corrections to the entorhinal cortex segmentation (when required). For this task I can create a entorhinal volume from ?h.entorhinal_exvivo.label using mri_label2vol This entorhinal volume will be different from the one in aparc+aseg.mgz My question is: Has anyone published any protocols to somehow combine the two entorhinal volumes ? Or is recommend to take the take the entorhinal volume created from ?h.entorhinal_exvivo.stats. and overlay it on norm.mgz and edit manually (when required). One limitation of this approach is that it would be hard to integrate this entorhinal volume back into aparc+aseg.mgz... Thanks Mehul On Wed, Dec 7, 2011 at 10:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Catherine I guess I would recommend the ex vivo one since it is based explicitly on architecontics and not on guessing locations from folds. cheers Bruce On Wed, 7 Dec 2011, Cat Chong wrote: Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine ___ 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] entorhinal cortex volume question
Thanks for quick response Bruce. We will use the volume from ex-vivo stats.. Regarding the need to integrate the ex vivo one back into aparc+aseg. We noticed the entorhinal volume in aparc is larger than that in exvivo.stats. So do the extra entorhinal voxels in aparc need to be re-labelled as unkown or as cortical-gray-matter? We plan to make manual correction on aparc (when required): So would it be a good approach to use the entorhinal labels from exvivo.stats to guide the corrections on aparc ? In this case, the question is, what should the end-user re-label the extra entorhinal voxels as ? Thanks Mehul On Tue, Jan 29, 2013 at 6:02 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Mehul the entorhinal label in the aparc was drawn by Rahul based on gyral landmarks. The one in the _exvivo.stats is based on being able to see the layer II islands in ex vivo MRI and hence we believe it is more accurate. Not sure why you need to integrate the ex vivo one back into the aparc+aseg, can you clarify? cheers Bruce On Tue, 29 Jan 2013, Mehul Sampat wrote: Hi Folks, I have a question about entorhinal cortex volume. The entorhinal cortex is listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous post on the mailing list, it was mentioned that we should use the volume measurement from ?h.entorhinal_exvivo.stats. We would like to make manual corrections to the entorhinal cortex segmentation (when required). For this task I can create a entorhinal volume from ?h.entorhinal_exvivo.label using mri_label2vol This entorhinal volume will be different from the one in aparc+aseg.mgz My question is: Has anyone published any protocols to somehow combine the two entorhinal volumes ? Or is recommend to take the take the entorhinal volume created from ?h.entorhinal_exvivo.stats. and overlay it on norm.mgz and edit manually (when required). One limitation of this approach is that it would be hard to integrate this entorhinal volume back into aparc+aseg.mgz... Thanks Mehul On Wed, Dec 7, 2011 at 10:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Catherine I guess I would recommend the ex vivo one since it is based explicitly on architecontics and not on guessing locations from folds. cheers Bruce On Wed, 7 Dec 2011, Cat Chong wrote: Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.
[Freesurfer] entorhinal cortex volume question
Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine___ 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] entorhinal cortex volume question
Hi Catherine I guess I would recommend the ex vivo one since it is based explicitly on architecontics and not on guessing locations from folds. cheers Bruce On Wed, 7 Dec 2011, Cat Chong wrote: Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine ___ 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.
