Dear Freesurfer experts,
I have processed my images and done analysis with cortical thickness using FS510. Now that I want to do vertex-wise analysis with surface area and volume, I learned that there is a bug in FS510 with this. ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.ht... ) Before I go on to use recon-all subject -qcache in FS530 to generate vertex-wise surface area and volume maps, I want to make sure that this would not cause concerns about use of mixed versions of Freesurfer, or concerns about interpreting my cortical thickness and surface area/volume findings together. And if it does, what should I do?
Thanks a lot, Cherry
It is ok to run -qcache using 5.3.
On 04/23/2014 10:54 PM, Yizhou Ma wrote:
Dear Freesurfer experts,
I have processed my images and done analysis with cortical thickness using FS510. Now that I want to do vertex-wise analysis with surface area and volume, I learned that there is a bug in FS510 with this. (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.ht...) Before I go on to use recon-all subject -qcache in FS530 to generate vertex-wise surface area and volume maps, I want to make sure that this would not cause concerns about use of mixed versions of Freesurfer, or concerns about interpreting my cortical thickness and surface area/volume findings together. And if it does, what should I do?
Thanks a lot, Cherry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Great. Thanks Doug.
On Thu, Apr 24, 2014 at 10:39 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
It is ok to run -qcache using 5.3.
On 04/23/2014 10:54 PM, Yizhou Ma wrote:
Dear Freesurfer experts,
I have processed my images and done analysis with cortical thickness using FS510. Now that I want to do vertex-wise analysis with surface area and volume, I learned that there is a bug in FS510 with this. (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.ht... )
Before I go on to use recon-all subject -qcache in FS530 to generate vertex-wise surface area and volume maps, I want to make sure that this would not cause concerns about use of mixed versions of Freesurfer, or concerns about interpreting my cortical thickness and surface area/volume findings together. And if it does, what should I do?
Thanks a lot, Cherry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Hi Doug,
To follow-up: I have been running recon-all subject -qcache but for some of my subjects it "exited with ERRORS" due to unmatched number of vertices. I read from previous threads that the general fix is to run -autorecon2 and -autorecon3 again. However, I hesitate to do that in my case due to the difference in Freesurfer versions. What do you think I can do?
Thanks, Cherry
On Thu, Apr 24, 2014 at 12:06 PM, Yizhou Ma ym850@nyu.edu wrote:
Great. Thanks Doug.
On Thu, Apr 24, 2014 at 10:39 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
It is ok to run -qcache using 5.3.
On 04/23/2014 10:54 PM, Yizhou Ma wrote:
Dear Freesurfer experts,
I have processed my images and done analysis with cortical thickness using FS510. Now that I want to do vertex-wise analysis with surface area and volume, I learned that there is a bug in FS510 with this. (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.ht... )
Before I go on to use recon-all subject -qcache in FS530 to generate vertex-wise surface area and volume maps, I want to make sure that this would not cause concerns about use of mixed versions of Freesurfer, or concerns about interpreting my cortical thickness and surface area/volume findings together. And if it does, what should I do?
Thanks a lot, Cherry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Run with those flags using the version of FS that you analyzed them with originally
On 04/25/2014 09:55 AM, Yizhou Ma wrote:
Hi Doug,
To follow-up: I have been running recon-all subject -qcache but for some of my subjects it "exited with ERRORS" due to unmatched number of vertices. I read from previous threads that the general fix is to run -autorecon2 and -autorecon3 again. However, I hesitate to do that in my case due to the difference in Freesurfer versions. What do you think I can do?
Thanks, Cherry
On Thu, Apr 24, 2014 at 12:06 PM, Yizhou Ma <ym850@nyu.edu mailto:ym850@nyu.edu> wrote:
Great. Thanks Doug. On Thu, Apr 24, 2014 at 10:39 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: It is ok to run -qcache using 5.3. On 04/23/2014 10:54 PM, Yizhou Ma wrote: > Dear Freesurfer experts, > > I have processed my images and done analysis with cortical thickness > using FS510. Now that I want to do vertex-wise analysis with surface > area and volume, I learned that there is a bug in FS510 with this. > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.html) > Before I go on to use recon-all subject -qcache in FS530 to generate > vertex-wise surface area and volume maps, I want to make sure that > this would not cause concerns about use of mixed versions of > Freesurfer, or concerns about interpreting my cortical thickness and > surface area/volume findings together. And if it does, what should I do? > > Thanks a lot, > Cherry > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Yizhou Ma