Dear all,

After running the recon-all on a subject, I needed to create a 'pial' surface to include the hippocampi, which are not included well in the pial reconstruction. So I generated a mask and used it to mask brain.mgz.

1. All well, except that in both the mask and the masked brain volume (readybrain.mgz, see below), the fill extends with a variable layer of about 1 voxel) above the pial red contour in some areas (see the top, leading me to believe that the red contours we use when editing are not the actual pial surfaces, but some interpolations of the actual calculated pial surface. If this is true, then there may be some editing errors when using these contours. Another explanation could be the resolution of the mris_fill.
Please let me know which is the case, and how to fix it so that the mask closely follows the red contour.

2. I need to generate a surface from readybrain.mgz, preferably that can be registered to the sphere.reg and on which cortical parcellation (DK atlass) can be applied. Is there a way? If not, I would still like to know how to generate the surface of this volume.

Thank you,

Octavian

Here is the code I used:

cd /usr/local/fs5.3/freesurfer/subjects/subjid

mris_fill -c -r 0.1 surf/rh.pial mri/rh.pial.filled.mgz && \
mris_fill -c -r 0.1 surf/lh.pial mri/lh.pial.filled.mgz && \
mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz --o mri/pial.filled.mgz && \
cd ./mri && \
mri_binarize --i aseg.mgz --match 5 --match 9 --match 10 --match 14 --match 17 --match 18 --match 19\
 --match 25 --match 31 --match 44 --match 48 --match 49 --match 53 --match 54 --match 55 --match 57\
 --match 63 --match 86 --match 96 --match 97 --match 105 --match 106 --match 114 --match 115\
 --match 195 --match 199 --match 203 --match 204 --match 205 --match 216 --match 222 --match 225\
 --match 507 --match 557 --match 1200 --match 1201 --match 1205 --match 1206 --match 2200 --match 2201\
 --match 2205 --match 2206 --o hippoamy.mask.mgz && \
fscalc pial.filled.mgz add hippoamy.mask.mgz -o epimask.mgz && \
mri_convert brain.mgz brain.float.mgz -odt float && \
mri_mask brain.float.mgz epimask.mgz readybrain.mgz