Dear FreeSurfers,
I have been working on cross-sectional MRI's of healthy older adults (55-88), and have been correcting the FreeSurfer 5.1 output using the instructions given here ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) to correct the FreeSurfer errors that we have found. For the majority of the subjects, we have been able to fix the errors as described by your website. However, for about 7 of our subjects, whenever we attempt to add WMCP to non-traced white matter regions (especially noticed in the anterior region of the temporal lobe), the new "main surface" and "Pial" tracings end up much worse than they were originally (thus, new problems that never previously existed are created). At this point we have tried a variety of things. We have tried going back to the original FreeSurfer Output to add WMCP differently, yet a variety of new problems are consistently being created (on some of these subjects we have tried over 10+ different ways of adding WMCP in order to fix the brains). After this has occured, we simply tried fixing the "new problems" as well, but it has created a never ending loop of new problems (upon fixing the new problems, even newer problems were created). For some of our subjects (besides these 7), this eventually leads to a correct segmentation. However, for these 7, we have been unable to ever end up at an adequate tracing?? I would love you send you images and or the files themselves to figure out how to proceed (however, when I tried to send it as an attachment my message was rejected due to size issures). Is there a way I can directly send you the FS output (via a ftp site, or dropbox) so you can look at the problem directly? The IRB has approved our "sharing" of this data if it helps us in our processing.
Also, do you have any suggestions on how we might proceed? Is there a way besides adding WMCP to assist our fixing of the anterior temporal regions? Thanks in advance.
Sincerely, Mark Fletcher
Hi Mark, Try either one of these options for uploading data or snapshots for us to look at.
FTP info: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
E-mail file drop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-Louis
On Mon, 20 Aug 2012, Mark Fletcher wrote:
Dear FreeSurfers,
I have been working on cross-sectional MRI's of healthy older adults (55-88), and have been correcting the FreeSurfer 5.1 output using the instructions given here(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDat a) to correct the FreeSurfer errors that we have found. For the majority of the subjects, we have been able to fix the errors as described by your website. However, for about 7 of our subjects, whenever we attempt to add WMCP to non-traced white matter regions (especially noticed in the anterior region of the temporal lobe), the new "main surface" and "Pial" tracings end up much worse than they were originally (thus, new problems that never previously existed are created). At this point we have tried a variety of things. We have tried going back to the original FreeSurfer Output to add WMCP differently, yet a variety of new problems are consistently being created (on some of these subjects we have tried over 10+ different ways of adding WMCP in order to fix the brains). After this has occured, we simply tried fixing the "new problems" as well, but it has created a never ending loop of new problems (upon fixing the new problems, even newer problems were created). For some of our subjects (besides these 7), this eventually leads to a correct segmentation. However, for these 7, we have been unable to ever end up at an adequate tracing?? I would love you send you images and or the files themselves to figure out how to proceed (however, when I tried to send it as an attachment my message was rejected due to size issures). Is there a way I can directly send you the FS output (via a ftp site, or dropbox) so you can look at the problem directly? The IRB has approved our "sharing" of this data if it helps us in our processing.
Also, do you have any suggestions on how we might proceed? Is there a way besides adding WMCP to assist our fixing of the anterior temporal regions? Thanks in advance.
Sincerely, Mark Fletcher
Hi Mark, Did you see my post from 1/10/2012 ("anterior temporal lobe problems")? We had good success (albeit not perfect) in improving our anterior temporal surfaces using the options mentioned there.
cheers, -MH
On Mon, 2012-08-20 at 14:43 -0500, Mark Fletcher wrote:
Dear FreeSurfers,
I have been working on cross-sectional MRI's of healthy older adults (55-88), and have been correcting the FreeSurfer 5.1 output using the instructions given here (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) to correct the FreeSurfer errors that we have found. For the majority of the subjects, we have been able to fix the errors as described by your website. However, for about 7 of our subjects, whenever we attempt to add WMCP to non-traced white matter regions (especially noticed in the anterior region of the temporal lobe), the new "main surface" and "Pial" tracings end up much worse than they were originally (thus, new problems that never previously existed are created). At this point we have tried a variety of things. We have tried going back to the original FreeSurfer Output to add WMCP differently, yet a variety of new problems are consistently being created (on some of these subjects we have tried over 10+ different ways of adding WMCP in order to fix the brains). After this has occured, we simply tried fixing the "new problems" as well, but it has created a never ending loop of new problems (upon fixing the new problems, even newer problems were created). For some of our subjects (besides these 7), this eventually leads to a correct segmentation. However, for these 7, we have been unable to ever end up at an adequate tracing?? I would love you send you images and or the files themselves to figure out how to proceed (however, when I tried to send it as an attachment my message was rejected due to size issures). Is there a way I can directly send you the FS output (via a ftp site, or dropbox) so you can look at the problem directly? The IRB has approved our "sharing" of this data if it helps us in our processing.
Also, do you have any suggestions on how we might proceed? Is there a way besides adding WMCP to assist our fixing of the anterior temporal regions? Thanks in advance.
Sincerely, Mark Fletcher _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Louis Nicholas Vinke -
Mark Fletcher -
Michael Harms