Hi All,
I'm having a problem related to that of Ed Gronensch (see below) with viewing the hippocampal subfields overlaid on the nu.mgz mri in Freeview. I recently installed the most recent version for FreeSurfer (lion for MAC). When I use the command listed on the website ( cd $SUBJECTS_DIR/bert/mri freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt) It says in the command console history "Can not find index for color name posterior_left_CA1". When I manually load the subfields through the GUI (by loading them as subsequent volumes), they load just fine, however there is no suitable color pallet this way because the subfield.mgz files are, as you know probabilistic and therefore even when I choose the Lookup Table color map, are shown in rainbow colors. It is clear that these colors are a reflection of the fact that the subfields are probabilistic, not labels. In other words, the value of the image varies on the 0-255 scale and the colors reflect these, rather than the subfields being different discrete colors due to all being part of a mask or something like that. I hope this makes sense. Any help you could provide would be incredibly appreciated. Thanks SO much.
Best, Mike
----------------------------------------------------------------------- Mike Strupp-Levitsky, BA Data Manager & Image Analyst Molecular Imaging & Neuropathology Division Columbia University, Department of Psychiatry New York State Psychiatric Institute, Suite 3920 (W): 212-543-5016 (C): 607-227-8811 Email: ms4637@columbia.edu