Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Hi all, This is a follow-up on my question so that people can know what I've tried and how it works. I added control points in the white matter and the delineation of the temporal lobe has improved to a satisfying level. We also find what Michael has suggested very interesting. But it seems that if we change the parameters for certain subjects, we would have to rerun all of the other subjects with the same set of parameters, which may not be desirable at the moment. Thanks for all the help, Cherry On Wed, May 22, 2013 at 4:46 PM, Yizhou Ma ym...@nyu.edu wrote: Hi Michael, This method seems cool. I'll try to implement it. Thank you so much. Best, Cherry On Wed, May 22, 2013 at 4:17 PM, Harms, Michael mha...@wustl.edu wrote: I've also posted in the past on a set of expert options that helped our surfaces in the temporal lobe considerably. You should be able to locate that post in the archives. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Yizhou Ma ym...@nyu.edu Date: Wednesday, May 22, 2013 2:30 PM To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu, Chris Watson christopher.wat...@childrens.harvard.edu Subject: Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz? Ok. I'll give it a try. Thanks, Chris Bruce! On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Cherry Chris is right. Putting control points in the WM will help the pial surface as well. cheers Bruce On Wed, 22 May 2013, Yizhou Ma wrote: Hi Chris, Thanks a lot. I agree that control points should actually only be put in white matter. I'm just not sure if I can expand the pial surface to a satisfactory extend if I only do edits in the white matter. It seems to me that the problem here is that the signal weakened in the lower part of the brain so that the gray matter doesn't have adequate intensity to be included in the pial surface (the values are around 30). Thanks, Cherry On Wed, May 22, 2013 at 3:14 PM, Chris Watson Christopher.Watson@childrens.**harvard.educhristopher.wat...@childrens.harvard.edu wrote: You need to place the control points in the white matter, not around it. On 05/22/2013 03:04 PM, Yizhou Ma wrote: Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**PialEditshttp://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry __**_ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
You need to place the control points in the white matter, not around it. On 05/22/2013 03:04 PM, Yizhou Ma wrote: Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry ___ 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] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Hi Chris, Thanks a lot. I agree that control points should actually only be put in white matter. I'm just not sure if I can expand the pial surface to a satisfactory extend if I only do edits in the white matter. It seems to me that the problem here is that the signal weakened in the lower part of the brain so that the gray matter doesn't have adequate intensity to be included in the pial surface (the values are around 30). Thanks, Cherry On Wed, May 22, 2013 at 3:14 PM, Chris Watson christopher.wat...@childrens.harvard.edu wrote: You need to place the control points in the white matter, not around it. On 05/22/2013 03:04 PM, Yizhou Ma wrote: Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Hi Cherry Chris is right. Putting control points in the WM will help the pial surface as well. cheers Bruce On Wed, 22 May 2013, Yizhou Ma wrote: Hi Chris, Thanks a lot. I agree that control points should actually only be put in white matter. I'm just not sure if I can expand the pial surface to a satisfactory extend if I only do edits in the white matter. It seems to me that the problem here is that the signal weakened in the lower part of the brain so that the gray matter doesn't have adequate intensity to be included in the pial surface (the values are around 30). Thanks, Cherry On Wed, May 22, 2013 at 3:14 PM, Chris Watson christopher.wat...@childrens.harvard.edu wrote: You need to place the control points in the white matter, not around it. On 05/22/2013 03:04 PM, Yizhou Ma wrote: Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Ok. I'll give it a try. Thanks, Chris Bruce! On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Cherry Chris is right. Putting control points in the WM will help the pial surface as well. cheers Bruce On Wed, 22 May 2013, Yizhou Ma wrote: Hi Chris, Thanks a lot. I agree that control points should actually only be put in white matter. I'm just not sure if I can expand the pial surface to a satisfactory extend if I only do edits in the white matter. It seems to me that the problem here is that the signal weakened in the lower part of the brain so that the gray matter doesn't have adequate intensity to be included in the pial surface (the values are around 30). Thanks, Cherry On Wed, May 22, 2013 at 3:14 PM, Chris Watson Christopher.Watson@childrens.**harvard.educhristopher.wat...@childrens.harvard.edu wrote: You need to place the control points in the white matter, not around it. On 05/22/2013 03:04 PM, Yizhou Ma wrote: Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**PialEditshttp://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry __**_ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Hi Michael, This method seems cool. I'll try to implement it. Thank you so much. Best, Cherry On Wed, May 22, 2013 at 4:17 PM, Harms, Michael mha...@wustl.edu wrote: I've also posted in the past on a set of expert options that helped our surfaces in the temporal lobe considerably. You should be able to locate that post in the archives. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Yizhou Ma ym...@nyu.edu Date: Wednesday, May 22, 2013 2:30 PM To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu, Chris Watson christopher.wat...@childrens.harvard.edu Subject: Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz? Ok. I'll give it a try. Thanks, Chris Bruce! On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Cherry Chris is right. Putting control points in the WM will help the pial surface as well. cheers Bruce On Wed, 22 May 2013, Yizhou Ma wrote: Hi Chris, Thanks a lot. I agree that control points should actually only be put in white matter. I'm just not sure if I can expand the pial surface to a satisfactory extend if I only do edits in the white matter. It seems to me that the problem here is that the signal weakened in the lower part of the brain so that the gray matter doesn't have adequate intensity to be included in the pial surface (the values are around 30). Thanks, Cherry On Wed, May 22, 2013 at 3:14 PM, Chris Watson Christopher.Watson@childrens.**harvard.educhristopher.wat...@childrens.harvard.edu wrote: You need to place the control points in the white matter, not around it. On 05/22/2013 03:04 PM, Yizhou Ma wrote: Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**PialEditshttp://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry __**_ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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.
