Hi Ana,
This email is probably best directed at the MNE list (cced), since you are
using an MNE command: mne_watershed_bem (even though it calls FS). To
answer your question. The first step would be to try playing with the
options in mne_watershed_bem (particularly --atlas
specify the --atlas option for mri_watershed
--gcaatlas use the subcortical atlas
--preflood number change the preflood height)
It will be a challenge to get this to work. I also recommend talking to
your MRI people about how noisy the data is. (even on a 12 ch. coil I would
expect less noise in my images, if there is nothing they can do I would
recommend collecting a second MPRAGE: for averaging). The other thing to
consider is collecting MEFLASH data to calculate your BEM (these data
provide much higher quality bem surfaces).
HTH
D
Hello,
I have some unexpected results from the mne_watershed_bem script that uses
Freesurfer mri_watershed program.For one of my subject's the inner scull surface ( xxxx_inner_scull_surface
in bem/watershed/) partially excludes cerebellum (the left screen shot).
All my other subjects have cerebellum included into the inner scull (right
screen shot). As a consequence later stage scripts (mne_setup_forward_model
and mne_do_forward_solution) produce similarly erroneous inner scull
surface delineation.Did anyone experience this problem before, and if so, how would you advise
to fix it?For this subject MRI MP RAGE sequence was acquired using the 12 channel
coil, which, compared to the 32 channel one used for other subjects,
produced images of worse quality. However, I have other subjects with 12
channel coil scans and their inner scull surfaces were separated normally
(including the cerebellum).Thanks,
Ana_______________________________________________
Freesurfer mailing list
Freesurfer at nmr.mgh.harvard.edu
Freesurfer Info PageThe 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
contains patient information, please contact the Partners Compliance
HelpLine at
MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140924/2219b2ba/attachment.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 24016 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140924/2219b2ba/attachment.jpe
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 25354 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140924/2219b2ba/attachment-0001.jpe