MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern
Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Mon, Aug 1, 2011 at 12:23 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
wrote:
how do you know left/right is correct? In any case, if you
upload the subject we'll take a look. Things very rarely fail
that badly
On Mon, 1 Aug 2011, Christopher Luna wrote:
Hi Bruce,
The orientations are correct - they weren't at first so I
had to do a lot of work in tkregister2 to get the
orientations correct. Unfortunately I only have access to
the
*.IMG and sometimes the *.HDR file for each subject.
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab,
McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Mon, Aug 1, 2011 at 12:16 PM, Bruce Fischl
<
fischl@nmr.mgh.harvard.edu> wrote:
Hi Christopher,
are you sure that the orientations are correct? That is,
when you bring the orig.mgz up in tkmedit does the coronal view
actually show the brain coronally? Img
is a dangerous format to use as it doesn't contain
orientation info. Do you have access to the data in some other
format before it was convered to img?
Bruce
On Mon, 1 Aug 2011, Christopher Luna wrote:
Hello Freesurfers,
I'm putting *.IMG files into the program and after correcting
talaraich transformations for them, I notice that when the
reconstructions have completed, that
there are
entire lobes of white matter absent from the surfaces detected
and from the wm.mgz file. I went through my hand at first to
manually fill in the missing white
matter for
the first case, but after seeing how many were affected, I
figured there was some setting I may be missing or some contrast
level that may be off.
I had tried using control points, but after following the WIKI
instructions on regenerating surfaces after placing them, I
found no significant difference in
white matter
detection.
How do I ensure all of the white matter in my converted IMGs is
identified?
Thank you kindly,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab,
McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
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