[Freesurfer] Altering the white matter low limit
Hello freesurfers, I wanted to get your opinion on altering the white matter low limit in the mri_segment command through attaching the -seg-wlo flag onto -autorecon2. I am working on a Frontotemporal Dementia cohort. In patients with severe atrophy, there always tends to be a great deal of both white matter and pial surface underestimation in the anterior temporal and dorsal frontal areas. I have found that lowering the white matter low limit does a fantastic job of fixing the surface underestimations in those regions-saving the numerous hours of labor required to manually fix these problem areas with control points. I was hoping someone could provide insight into what exactly changing this value is doing to the data. Does changing this value lead to inaccuracies that I am not seeing? Most importantly, is it safe to mix cases where I set the white matter low limit to 60 (or 40 in some severe cases) with other cases that retain their default value of 90 in the same dataset? Thank you! Gabe Gabe Marx Clinical Research Coordinator UCSF Memory Aging Center 675 Nelson Rising Lane, Suite 190 San Francisco, CA 94158 T: (415) 476-3861 ___ 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] Using the -seg-wlo option
Hello freesurfers, I wanted to get your opinion on altering the white matter low limit in the mri_segment command through attaching the -seg-wlo flag onto -autorecon2. I am working on a Frontotemporal Dementia cohort. In patients with severe atrophy, there always tends to be a great deal of both white matter and pial surface underestimation in the anterior temporal and dorsal frontal areas. I have found that lowering the white matter low limit does a fantastic job of fixing the surface underestimations in those regions-saving the numerous hours of labor required to manually fix these problem areas with control points. I was hoping someone could provide insight into what exactly changing this value is doing to the data. Does changing this value lead to inaccuracies that I am not seeing? Most importantly, is it safe to mix cases where I set the white matter low limit to 60 (or 40 in some severe cases) with other cases that retain their default value of 90 in the same dataset? Thank you! Gabe Gabe Marx Clinical Research Coordinator UCSF Memory Aging Center 675 Nelson Rising Lane, Suite 190 San Francisco, CA 94158 T: (415) 476-3861 ___ 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] v5.1 control point mri_ca_normalize bug
Thank you for your help! So you are suggesting that after we insert the patch we run -autorecon2 -autorecon3 -clean-aseg on all of the subjects who were previously run with the -nocanorm flag? How will this affect the edits previously made on them? Thank you, Gabe -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH Sent: Sunday, October 12, 2014 12:14 PM To: Bruce Fischl Cc: Freesurfer support list Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug correct (the thing to do is comment-out the addition of the control points). n. On Wed, 2014-10-08 at 17:05 -0400, Bruce Fischl wrote: I don't think you want to run with -nocanorm. Just commenting out the addition of the -f $ControlPointsFile should be sufficient. Right Nick? On Wed, 8 Oct 2014, Marx, Gabe wrote: Hi Bruce, I appreciate the response! I am sorry, I am a bit confused. The release notes state: An option is to disable the running of mri_ca_normalize when re-running the -autorecon2 or -autorecon2-cp stage after adding control points by adding the flag -nocanorm to the end of recon-all. We will continue to investigate a more automated solution to detection of this problem. The more permanent workaround for v5.1 users is to edit their recon-all script making the following change, which will disable usage of control points with ca_norm: # find these lines: set cmd = (mri_ca_normalize) if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # and comment-out the second line like this: set cmd = (mri_ca_normalize) #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # then re-run your subjects with the flags: -autorecon2 -autorecon3 -clean-aseg Are you saying the -nocanorm flag will result in inaccurate data? Thanks! Gabe -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, October 08, 2014 8:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug Hi Gabe this wasn't really a bug per-se, just induced some behavior that people didn't like. You can't skip the mri_ca_normalize step or the aseg won't be accurate. The aseg patch I believe just starts autorecon2-cp after the aseg hs been created, but Nick or Zeke can correct me if I'm wrong. cheers Bruce On Mon, 6 Oct 2014, Marx, Gabe wrote: Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the –nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize in my pipeline. Would someone be able to give me a better description as to what mri_ca_normalize is doing and what I am sacrificing by taking it out of my pipeline? Furthermore, in regards to the patch for the recon-all script to fix this bug, what is the patch doing exactly? If I had some data in which I used the –nocanorm flag and other data in which I used the patch would I still be able to make valid analysis if I merged them? Would there be significant inconsistencies? Thanks! Best, Gabe ___ 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
Re: [Freesurfer] v5.1 control point mri_ca_normalize bug
Hi Bruce, I appreciate the response! I am sorry, I am a bit confused. The release notes state: An option is to disable the running of mri_ca_normalize when re-running the -autorecon2 or -autorecon2-cp stage after adding control points by adding the flag -nocanorm to the end of recon-all. We will continue to investigate a more automated solution to detection of this problem. The more permanent workaround for v5.1 users is to edit their recon-all script making the following change, which will disable usage of control points with ca_norm: # find these lines: set cmd = (mri_ca_normalize) if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # and comment-out the second line like this: set cmd = (mri_ca_normalize) #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # then re-run your subjects with the flags: -autorecon2 -autorecon3 -clean-aseg Are you saying the -nocanorm flag will result in inaccurate data? Thanks! Gabe -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, October 08, 2014 8:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug Hi Gabe this wasn't really a bug per-se, just induced some behavior that people didn't like. You can't skip the mri_ca_normalize step or the aseg won't be accurate. The aseg patch I believe just starts autorecon2-cp after the aseg hs been created, but Nick or Zeke can correct me if I'm wrong. cheers Bruce On Mon, 6 Oct 2014, Marx, Gabe wrote: Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the –nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize in my pipeline. Would someone be able to give me a better description as to what mri_ca_normalize is doing and what I am sacrificing by taking it out of my pipeline? Furthermore, in regards to the patch for the recon-all script to fix this bug, what is the patch doing exactly? If I had some data in which I used the –nocanorm flag and other data in which I used the patch would I still be able to make valid analysis if I merged them? Would there be significant inconsistencies? Thanks! Best, Gabe ___ 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] v5.1 control point mri_ca_normalize bug
Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the -nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize in my pipeline. Would someone be able to give me a better description as to what mri_ca_normalize is doing and what I am sacrificing by taking it out of my pipeline? Furthermore, in regards to the patch for the recon-all script to fix this bug, what is the patch doing exactly? If I had some data in which I used the -nocanorm flag and other data in which I used the patch would I still be able to make valid analysis if I merged them? Would there be significant inconsistencies? Thanks! Best, Gabe ___ 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.
