Hello, I am trying to run cortical thickness on a few scans. After the initial recon-all -all command not all regions of grey and white matter were included. I have attached a picture of the problem (the right side temporal lobe is not included, but the the left side is). I tried adding control points and re-running the process with the command "-autorecon-all -autorecon2-cp -autorecon3 -subjid *subject name" *but I do not get a very improved result. If there anything else I can try?
Thank you for all your help, Kristina Nalbandyan Neuroscience Undergraduate Interdepartmental Program, UCLA
Hi Kristina
I would guess you have a topological defect that is being fixed incorrectly. If you upload the subject I'm happy to take a look (in between rounds of shoveling)
Bruce On Fri, 8 Feb 2013, Kristina Nalbandian wrote:
Hello, I am trying to run cortical thickness on a few scans. After the initial recon-all -all command not all regions of grey and white matter were included. I have attached a picture of the problem (the right side temporal lobe is not included, but the the left side is). I tried adding control points and re-running the process with the command "-autorecon-all -autorecon2-cp -autorecon3 -subjid subject name" but I do not get a very improved result. If there anything else I can try?
Thank you for all your help, Kristina Nalbandyan Neuroscience Undergraduate Interdepartmental Program, UCLA
Kristina, you can also run defect-seg to create aseg segmentation of the defects. Follow the instructions in the --help to visualize. Look in that region for defects. doug
On 2/8/13 5:56 PM, Bruce Fischl wrote:
Hi Kristina
I would guess you have a topological defect that is being fixed incorrectly. If you upload the subject I'm happy to take a look (in between rounds of shoveling)
Bruce On Fri, 8 Feb 2013, Kristina Nalbandian wrote:
Hello, I am trying to run cortical thickness on a few scans. After the initial recon-all -all command not all regions of grey and white matter were included. I have attached a picture of the problem (the right side temporal lobe is not included, but the the left side is). I tried adding control points and re-running the process with the command "-autorecon-all -autorecon2-cp -autorecon3 -subjid subject name" but I do not get a very improved result. If there anything else I can try?
Thank you for all your help, Kristina Nalbandyan Neuroscience Undergraduate Interdepartmental Program, UCLA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for the reply! What is the command for running defect-seg? Will this only help me visualize the defects or will it correct them as well?
Many thanks
On Fri, Feb 8, 2013 at 3:25 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Kristina, you can also run defect-seg to create aseg segmentation of the defects. Follow the instructions in the --help to visualize. Look in that region for defects. doug
On 2/8/13 5:56 PM, Bruce Fischl wrote:
Hi Kristina
I would guess you have a topological defect that is being fixed incorrectly. If you upload the subject I'm happy to take a look (in between rounds of shoveling)
Bruce On Fri, 8 Feb 2013, Kristina Nalbandian wrote:
Hello, I am trying to run cortical thickness on a few scans. After the initial recon-all -all command not all regions of grey and white matter were included. I have attached a picture of the problem (the right side temporal lobe is not included, but the the left side is). I tried adding control points and re-running the process with the command "-autorecon-all -autorecon2-cp -autorecon3 -subjid subject name" but I do not get a very improved result. If there anything else I can try?
Thank you for all your help, Kristina Nalbandyan Neuroscience Undergraduate Interdepartmental Program, UCLA
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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it definitely won't correct them (otherwise we would have included it in recon-all already). We are correcting them, just not the right way (e.g. cutting instead of filling or visa-versa)
cheers Bruce
On Mon, 11 Feb 2013, Kristina Nalbandian wrote:
Thank you for the reply! What is the command for running defect-seg? Will this only help me visualize the defects or will it correct them as well?
Many thanks
On Fri, Feb 8, 2013 at 3:25 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote: Kristina, you can also run defect-seg to create aseg segmentation of the defects. Follow the instructions in the --help to visualize. Look in that region for defects. doug
On 2/8/13 5:56 PM, Bruce Fischl wrote: Hi Kristina I would guess you have a topological defect that is being fixed incorrectly. If you upload the subject I'm happy to take a look (in between rounds of shoveling) Bruce On Fri, 8 Feb 2013, Kristina Nalbandian wrote: Hello, I am trying to run cortical thickness on a few scans. After the initial recon-all -all command not all regions of grey and white matter were included. I have attached a picture of the problem (the right side temporal lobe is not included, but the the left side is). I tried adding control points and re-running the process with the command "-autorecon-all -autorecon2-cp -autorecon3 -subjid subject name" but I do not get a very improved result. If there anything else I can try? Thank you for all your help, Kristina Nalbandyan Neuroscience Undergraduate Interdepartmental Program, UCLA
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.
The command is defect-seg doug On 02/11/2013 03:09 PM, Kristina Nalbandian wrote:
Thank you for the reply! What is the command for running defect-seg? Will this only help me visualize the defects or will it correct them as well?
Many thanks
On Fri, Feb 8, 2013 at 3:25 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Kristina, you can also run defect-seg to create aseg segmentation of the defects. Follow the instructions in the --help to visualize. Look in that region for defects. doug On 2/8/13 5:56 PM, Bruce Fischl wrote:Hi Kristina I would guess you have a topological defect that is being fixed incorrectly. If you upload the subject I'm happy to take a look (in between rounds of shoveling) Bruce On Fri, 8 Feb 2013, Kristina Nalbandian wrote:Hello, I am trying to run cortical thickness on a few scans. After the initial recon-all -all command not all regions of grey and white matter were included. I have attached a picture of the problem (the right side temporal lobe is not included, but the the left side is). I tried adding control points and re-running the process with the command "-autorecon-all -autorecon2-cp -autorecon3 -subjid subject name" but I do not get a very improved result. If there anything else I can try? Thank you for all your help, Kristina Nalbandyan Neuroscience Undergraduate Interdepartmental Program, UCLA_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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