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