I think if you convert the afni's skull stripping to .mgz format and put
it in mri/brainmask.mgz we will recognize that it is different from
brainmask.auto.mgz and use it instead
cheers
Bruce
On Wed, 12 Jul 2017, Michelle
VanTieghem wrote:
Hi, I am just following up on my previous question.
The -gcut does not appear to make any difference on our skull stripping. I
also saw that you can change flags for watershed option. Do you recommend
this? If so, how would you implement this on freesurfer output that was
already run?
We achieve fairly good skull stripping with this dataset using afni's
skullstrip function. Would it be possible to enter the already-skull
stripped data into freesurfer? if so, how would you set this up? Right now,
I am entering the original dicom files as input to freesurfer -- is it
possible to use other file formats as input?
Thanks!
On Tue, Jul 4, 2017 at 12:43 PM, Michelle VanTieghem
<michelle.vantieg...@gmail.com> wrote:
Hello,
I am just following up on this question.
Thanks!
Michelle
On Tue, Jun 27, 2017 at 4:46 PM, Michelle VanTieghem
<michelle.vantieg...@gmail.com> wrote:
Hi Bruce,
The -gcut does not appear to make any difference on our skull
stripping. I also saw that you can change flags for watershed
option. Do you recommend this? If so, how would you implement
this on freesurfer output that was already run?
We achieve fairly good skull stripping with this dataset using
afni's skullstrip function. Would it be possible to enter the
already-skull stripped data into freesurfer? if so, how would
you set this up? Right now, I am entering the original dicom
files as input to freesurfer -- is it possible to use other file
formats as input?
Thanks!
Michelle
On Mon, Jun 12, 2017 at 4:49 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
-gcut should do the trick
cheers
Bruce
On Mon, 12 Jun 2017, Michelle VanTieghem wrote:
Hi,
Thanks for your response. Maybe I am
missing something, but I haven't been
able to find any documentation about how
to use graph cuts skull stripping
in the freesurfer pipeline. can you
please advise?
Thanks,
Michelle
On Mon, Jun 12, 2017 at 2:48 PM, Bruce
Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Michelle
you can try using the graph cuts
skull stripping. It is more
aggressive and more likely to
remove more skull/dura (and also
to remove some brain)
cheers
Bruce
On Mon, 12 Jun 2017, Michelle
VanTieghem wrote:
Hello,
We have assessed freesurfer
output for 160+ brains,
and about 50% have poor
segmentation of pial matter
that includes too much
skull. Manual edits and
re-running does work to
improve the problem, but is
very time/labor
intensive for so many scans.
I saw on the freesurfer wiki
that you can include T2
or Flair images to
improve the segmentation for
this problem. However,
we do not have these
extra scans. What do you
recommend to do otherwise?
Thank you!
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective
Neuroscience Lab
Columbia University
mrv2...@columbia.edu
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Columbia University
mrv2...@columbia.edu
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the sender and properly
dispose of the e-mail.
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
_______________________________________________
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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
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