We have been using the version 5.1 to do some longitudinal processing on a Mac computer using Lion.
Our template results have several areas that concern us and we are wondering the best approach for editing. We believe it is edit the pial surfaces in tkmedit. However, the tutorials are a bit confusing as they seem to contain slightly different steps and in neither place do they provide the kind of detail (i.e., which editing tool to use in tkmedit and if there are any configuration changes needed).
We have posted the following screen captures. The first shows is from free view and shows that strange lines in the hippocampus. The last two show attempts at editing but in the posterior part of the brain in the inter hemispheric fissure.
Any help would be greatly appreciated.
Thanks,
[cid:3A68F9FB-CA43-46B6-8D1B-8F0F42243677@v3.uthscsa.edu] [cid:4483FB3B-AB38-4350-973B-A800BD6FD3CA@v3.uthscsa.edu] [cid:220E38D7-5796-47E4-BDE5-DDB75CB6E2AE@v3.uthscsa.edu]
Hi David, You can edit in freeview or in tkmedit, it doesn't matter which one. The strange lines in the hippocampus are normal. The surfaces aren't used to measure subcortical volume and so they are not doing anything meaninful in those areas and may look a little strange.
I'm not so sure what you're trying to do with the second edit. If you send me the case, I can take a look. Allison
We have been using the version 5.1 to do some longitudinal processing on a Mac computer using Lion.
Our template results have several areas that concern us and we are wonderin g the best approach for editing. We believe it is edit the pial surfaces i n tkmedit. However, the tutorials are a bit confusing as they seem to conta in slightly different steps and in neither place do they provide the kind o f detail (i.e., which editing tool to use in tkmedit and if there are any c onfiguration changes needed).
We have posted the following screen captures. The first shows is from free view and shows that strange lines in the hippocampus. The last two show a ttempts at editing but in the posterior part of the brain in the inter hemi spheric fissure.
Any help would be greatly appreciated.
Thanks,
[cid:3A68F9FB-CA43-46B6-8D1B-8F0F42243677@v3.uthscsa.edu]
[cid:4483FB3B-AB38-4350-973B-A800BD6FD3CA@v3.uthscsa.edu]
[cid:220E38D7-5796-47E4-BDE5-DDB75CB6E2AE@v3.uthscsa.edu]
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Thanks Allison for your answer. We posted this on the list serve and saw it there for about one day. Then when we tried to follow up a few days later, it did not show up on the list serve. I was a little worried that I had posted something wrong.
Yes, I could upload a case for you. Just let me know where you would like me to send it.
In the second edit question, we were concerned about the pial surfaces in the inter hemispheric fissure. There are several place where the surface deviates into the gray matter at weird angles and persists for several slices.
Thanks for any help you can provide on this.
David
David F. Tate, Ph.D. Research Neuropsychologist Henry Jackson Foundation Contractor Defense and Veteran Brain Injury Centers San Antonio Military Medical Center San Antonio, TX
Assistant Professor of Radiology Research Imaging Institute University of Texas Health Science Center San Antonio 8403 Floyd Curl Drive San Antonio, TX 78249
210.567.8109
tatedf@uthscsa.edumailto:tatedf@uthscsa.edu
On Apr 6, 2012, at 10:24 AM, Allison Stevens Player wrote:
Hi David, You can edit in freeview or in tkmedit, it doesn't matter which one. The strange lines in the hippocampus are normal. The surfaces aren't used to measure subcortical volume and so they are not doing anything meaninful in those areas and may look a little strange.
I'm not so sure what you're trying to do with the second edit. If you send me the case, I can take a look. Allison
We have been using the version 5.1 to do some longitudinal processing on a Mac computer using Lion.
Our template results have several areas that concern us and we are won dering the best approach for editing. We believe it is edit the pial surfaces in tkmedit. However, the tutorials are a bit confusing as they see m to contain slightly different steps and in neither place do they provide the kind of detail (i.e., which editi ng tool to use in tkmedit and if there are any configuration changes needed ).
We have posted the following screen captures. The first shows is from free view and shows that strange lines in the hippocampus. The last two show attempts at editing but in the posterior part of the brain in the inter hemispheric fissure.
Any help would be greatly appreciated.
Thanks,
<Screen Shot 2012-03-02 at 3.41.56 PM.png> <Screen Shot 2012-03-05 at 3.15.16 PM.png> <Screen Shot 2012-03-05 at 3.15.01 PM.png> _______________________________________________
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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.
Hi David, You can send us the case via ftp or filedrop. See wiki page below.
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
-Louis
On Mon, 9 Apr 2012, Tate, David Franklin wrote:
Thanks Allison for your answer. We posted this on the list serve and saw it there for about one day. Then when we tried to follow up a few days later, it did not show up on the list serve. I was a little worried that I had posted something wrong.
Yes, I could upload a case for you. Just let me know where you would like me to send it.
In the second edit question, we were concerned about the pial surfaces in the inter hemispheric fissure. There are several place where the surface deviates into the gray matter at weird angles and persists for several slices.
Thanks for any help you can provide on this.
David
David F. Tate, Ph.D. Research Neuropsychologist Henry Jackson Foundation Contractor Defense and Veteran Brain Injury Centers San Antonio Military Medical Center San Antonio, TX
Assistant Professor of Radiology Research Imaging Institute University of Texas Health Science Center San Antonio 8403 Floyd Curl Drive San Antonio, TX 78249
210.567.8109
tatedf@uthscsa.edumailto:tatedf@uthscsa.edu
On Apr 6, 2012, at 10:24 AM, Allison Stevens Player wrote:
Hi David, You can edit in freeview or in tkmedit, it doesn't matter which one. The strange lines in the hippocampus are normal. The surfaces aren't used to measure subcortical volume and so they are not doing anything meaninful in those areas and may look a little strange.
I'm not so sure what you're trying to do with the second edit. If you send me the case, I can take a look. Allison
We have been using the version 5.1 to do some longitudinal processing on a Mac computer using Lion.
Our template results have several areas that concern us and we are won dering the best approach for editing. We believe it is edit the pial surfaces in tkmedit. However, the tutorials are a bit confusing as they see m to contain slightly different steps and in neither place do they provide the kind of detail (i.e., which editi ng tool to use in tkmedit and if there are any configuration changes needed ).
We have posted the following screen captures. The first shows is from free view and shows that strange lines in the hippocampus. The last two show attempts at editing but in the posterior part of the brain in the inter hemispheric fissure.
Any help would be greatly appreciated.
Thanks,
<Screen Shot 2012-03-02 at 3.41.56 PM.png> <Screen Shot 2012-03-05 at 3.15.16 PM.png> <Screen Shot 2012-03-05 at 3.15.01 PM.png> _______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto: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@nmr.mgh.harvard.edu
-
Allison Stevens Player -
Louis Nicholas Vinke -
Tate, David Franklin