Great Keith! Thanks for letting us know what worked for you.
On Wed, Jan 27, 2016 at 3:49 PM, Keith Doelling kd889@nyu.edu wrote:
Sorry. I appear to have figured out that my tolerance setting in the flood fill window was set to 0%. I increased it to 90% and that solved the problem. Thanks!
Keith
Keith Doelling Dept of Psychology Center for Neural Science NYU
science.keithdoelling.com
On Wed, Jan 27, 2016 at 3:29 PM, Keith Doelling kd889@nyu.edu wrote:
I can't figure out why i'm struggling with this fake layer of skin thing. I chose a slice about 7mm below the outer skull I made a polyline using the voxel edit window around the edges but when I try to control + click to fill in the space it only whitens the few voxels directly underneath the click area. Perhaps this is because I am using a mac? I can't find any setting that allows me to just create a solid disk as you mentioned. What am I missing here?
Thanks again for your help! Keith
Keith Doelling Dept of Psychology Center for Neural Science NYU
science.keithdoelling.com
On Tue, Jan 26, 2016 at 4:53 PM, dgw dgwakeman@gmail.com wrote:
That does look far enough, but you have a lot of signal dropout at the bottom of the scan. This could be due to poor alignment (the laser step when putting the person in the scanner), or your MR acquisition settings had the lower coils turned off (all of the receive coils should be on: sometimes other groups mess with the settings, which can affect your scans) , or the head coil has insufficient coverage of the lower part of the head (least likely).
To fix this I would just draw a fake skin layer. Simply load up your outer skull surface on the volume in freeview, then make sure that you generate a fake skin surface (the shape doesn't really matter, so a disk (which is the easiest) is fine). I would start ~ 7mm below the bottom edge of the outer skull surface and just paint a bunch of solid disks in the axial plane of the neck at value 255.
re-run the watershed bem and you should be good to go.
hth d
On Tue, Jan 26, 2016 at 3:10 PM, Keith Doelling kd889@nyu.edu wrote:
Here also is an image of the T1 if that's helpful. For future reference, is this not far enough below the cerebellum?
Thanks again!
https://dl.dropboxusercontent.com/u/5190414/T1.jpg [image: Inline image 1]
Keith Doelling Dept of Psychology Center for Neural Science NYU
science.keithdoelling.com
On Tue, Jan 26, 2016 at 2:47 PM, Keith Doelling kd889@nyu.edu wrote:
Sorry that was actually the outer skin and the inner skull. Here's all three: outer skin in cyan, outer skull in yellow and inner skull in red. Does mean I will need to draw in the bone as well as skin? Is there some documentation I can look at that would explain the best way for me to go about this?
Thanks for your help and for the quick reply!
https://dl.dropboxusercontent.com/u/5190414/skulloverlap2.png [image: Inline image 1]
Keith Doelling Dept of Psychology Center for Neural Science NYU
science.keithdoelling.com
On Tue, Jan 26, 2016 at 2:20 PM, dgw dgwakeman@gmail.com wrote:
Hi Keith,
The problem is actually the outer_skin crossing the outer_skull surface (from the images you show). For future data you will want to do a better job aligning the slices for the MRI to make sure you are well below the cerebellum in your coverage.
For this participant's data. you can load up the T1 in freeview, and edit the voxels at the base of the head to draw in a skin layer well below the cerebellum that connects to the person's skin at the neck.
hth d
On Tue, Jan 26, 2016 at 2:14 PM, Keith Doelling kd889@nyu.edu wrote:
> Hi All, > > I'm trying to source localize MEG data in MNE-Python but have run > across an issue with a subject's MRI in the freesurfer watershed algorithm. > Namely, the outer skull surface ever so slightly overlaps with the inner > skull (I've plotted this in freeview for your viewing pleasure). This is a > problem as MNE stops with an error in the make_bem_model function when such > overlap occurs (understandably). > > I have tried deleting the bottom slices of the T1.mgz and rerunning > the watershed algorithm but that actually made the overlap worse. I have > also tried using the -atlas parameter which made it a bit better but not > quite (that's actually what is plotted). What I would really like to do at > this point is manually edit the surfaces to avoid the overlap which I think > given the location and minuscule nature of the overlap. > > Any tips on how to get this done? Or on how to edit the MRI to avoid > this overlap to begin with? > > Thanks for your help! > Keith > https://dl.dropboxusercontent.com/u/5190414/skulloverlap.png > > [image: Inline image 1] > > Keith Doelling > Dept of Psychology > Center for Neural Science > NYU > > science.keithdoelling.com > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > >
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