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
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