Dear Freesurfer Team,
I have about 200 T1 coronal scans that were obtained with some shading in the frontal and occipital regions. Not sure if it can be seen from the attached picture, but the image fades toward the top and bottom (on the axial view). The segmentation left out a large section of the frontal and occipital, probably because the signal loss brings those voxels below the threshold for white and gray matter.
I have tried to run FSL bias correction and got a small improvement, but I wonder if there is any way these faded slides can be corrected so that the segmentation is capable of seeing these as proper white and gray matter.
In the attached picture, the blue is the wm surface and the red is the gray matter (wm and pial surfaces)
The image shown is actually the T1.mgz from freesufer that has already gone through the nu_correct step in recon_all, the original image looks very similar...
Thanks
Gabriel