[Mne_analysis] [Freesurfer] watershed problem

[dgw]

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



On Wed, Sep 24, 2014 at 10:17 AM, Anastasia Klimovich-Smith <ak798 at cam.ac.uk
> wrote:

>  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
>
>
>
>
>
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