Hello,
I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer.
I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner.
In BrainSuite, their are marked decreases in cortical thickness that is consistent with the patients TBI.
In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect.
Is there a way to post images? Or perhaps links to images on another site?
I am not sure where to begin to search for answers as to why I am getting these differences.
I would be happy to answer more questions - I likely have not provided enough information.
James Patterson
Hi James
sure, we'll take a look. Can you clarify what you are doing though? When you say there is decreased thickness what is it relative to? Information on uploading is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce
On Sat, 8 Sep 2012, Patterson, James wrote:
Hello,
I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer.
I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner.
In BrainSuite, their are marked decreases in cortical thickness that is
consistent with the patients TBI.
In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect.
Is there a way to post images? Or perhaps links to images on another site?
I am not sure where to begin to search for answers as to why I am getting these differences.
I would be happy to answer more questions - I likely have not provided enough information.
James Patterson _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Bruce,
Sorry for the delay, just getting back from Germany.
I have uploaded a PPT describing the issues that I am having - see notes in the PPT. They are under transfer/incoming, a TGZ file and a PPTZ file both dated today.
I also uploaded the data directory from the qdec evaluation.
Thanks, James
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Saturday, September 08, 2012 9:56 AM To: Patterson, James Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Hi James
sure, we'll take a look. Can you clarify what you are doing though? When you say there is decreased thickness what is it relative to? Information on uploading is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce
On Sat, 8 Sep 2012, Patterson, James wrote:
Hello,
I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer.
I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner.
In BrainSuite, their are marked decreases in cortical thickness that is
consistent with the patients TBI.
In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect.
Is there a way to post images? Or perhaps links to images on another site?
I am not sure where to begin to search for answers as to why I am getting these differences.
I would be happy to answer more questions - I likely have not provided enough information.
James Patterson _______________________________________________ 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 James
can you also upload the subject data? Tar and gzip the entire subject dir and then email us the coords where you think things are wrong in FreeSurfer?
cheers Bruce On Sun, 9 Sep 2012, Patterson, James wrote:
Thank you Bruce,
Sorry for the delay, just getting back from Germany.
I have uploaded a PPT describing the issues that I am having - see notes in the PPT. They are under transfer/incoming, a TGZ file and a PPTZ file both dated today.
I also uploaded the data directory from the qdec evaluation.
Thanks, James
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Saturday, September 08, 2012 9:56 AM To: Patterson, James Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Hi James
sure, we'll take a look. Can you clarify what you are doing though? When you say there is decreased thickness what is it relative to? Information on uploading is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce
On Sat, 8 Sep 2012, Patterson, James wrote:
Hello,
I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer.
I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner.
In BrainSuite, their are marked decreases in cortical thickness that is
consistent with the patients TBI.
In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect.
Is there a way to post images? Or perhaps links to images on another site?
I am not sure where to begin to search for answers as to why I am getting these differences.
I would be happy to answer more questions - I likely have not provided enough information.
James Patterson _______________________________________________ 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
OK, it's been uploaded.
--- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport ---
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, September 09, 2012 11:53 AM To: Patterson, James Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Hi James
can you also upload the subject data? Tar and gzip the entire subject dir and then email us the coords where you think things are wrong in FreeSurfer?
cheers Bruce On Sun, 9 Sep 2012, Patterson, James wrote:
Thank you Bruce,
Sorry for the delay, just getting back from Germany.
I have uploaded a PPT describing the issues that I am having - see notes in the PPT. They are under transfer/incoming, a TGZ file and a PPTZ file both dated today.
I also uploaded the data directory from the qdec evaluation.
Thanks, James
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Saturday, September 08, 2012 9:56 AM To: Patterson, James Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Hi James
sure, we'll take a look. Can you clarify what you are doing though? When you say there is decreased thickness what is it relative to? Information on uploading is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce
On Sat, 8 Sep 2012, Patterson, James wrote:
Hello,
I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer.
I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner.
In BrainSuite, their are marked decreases in cortical thickness that is
consistent with the patients TBI.
In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect.
Is there a way to post images? Or perhaps links to images on another site?
I am not sure where to begin to search for answers as to why I am getting these differences.
I would be happy to answer more questions - I likely have not provided enough information.
James Patterson _______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Patterson, James