詳細不明ですが、脳を膨らませる(dilate3D)、というのとtriangulate3Dで5-6mm(side length)のメッシュがよいという情報は有用かも知れません。
martinos.org/mne/manual/AppA.htmlよりコピペです
The brain segmentation provided by FreeSurfer in the directory mri/brain can be employed to create the inner skull surface triangulation with help of seglab, the Neuromag MRI segmentation tool. The description below assumes that the user is familiar with the seglab tool. If necessary, consult the seglab manual, Neuromag P/N NM20420A-A.
The data set mri/brain typically contains tissues within or outside the skull, in particular around the eyes. These must be removed manually before the inner skull triangulation is created.The editing and triangulation can be accomplished as outlined below
1. Set up the MRIs for Neuromag software access
Run the mne_setup_mri too as described in Setting up the anatomical MR images for MRIlab. As a result, the directories mri/T1-neuromag and mri/brain-neuromag are set up.
2. Load the MRI data
Open the file mri/brain-neuromag/sets/COR.fif and adjust the scaling of the data.
3. Preparatory steps
Set the minimum data value to 1 using the min3D operator. Make a backup of the data with the backup3D operator.
4. Manual editing
The maskDraw3D operation is recommended for manual editing. To use it, first employ the grow3D operator with threshold interval 2...255 and the seed point inside the brain. Then do the editing in the slicer window as described in Section 5.4.2 of the seglab manual. Note that it is enough to remove the connectivity to the extracerebral tissues rather than erasing them completely.
5. Grow again and mask
Once manual editing is complete, employ the grow3D operator again and do mask3D with the backup data to see whether the result is satisfactory. If not, undo mask3D and continue manual editing. Otherwise, undo mask3D and proceed to the next step.
6. Dilation
It is advisable to make the inner skull surface slightly bigger than the brain envelope obtained in the previous step. Therefore, apply the dilate3D operation once or twice. Use the values 1 for nbours and 26 for nhood in the first dilation and 1 and 18 in the second one, respectively.
7. Triangulation
Triangulate the resulting object with the triangulate3D operator. Use a sidelength of 5 to 6 mm. Check that the triangulation looks reasonable in the 3D viewing window.
8. Save the triangulation
Save the triangulated surface as a mesh into bem/inner_skull.tri. Select unit of measure as millimeters and employ the MRI coordinate system.