Training:Workshop Sept16 2005 Freesurfer List

Workshop attendees feel free to add to this list, please send an e-mail to Sonia Pujol (spujol@bwh.harvard.edu) if you do, so that we pay attention.

• From Slicer, load in ASEG volume so you can see the whole brain color coded by structure. Question: Any problems with how to handle the ColorMap so that the user knows what structure each color corresponds too?

• Load in the T1.mgz or brain.mgz volumes along with the ASEG.mgz volume so you can view the color transparently over the black and white brain. Use of this is to assess the quality of the segmentation, this is what Brad Dickerson has been repeatedly requesting.

• Build models from the ASEG volume such that each structure has its own model (Steve Pieper says do this in one step for all the structures simultaneously to get the best boundaries between structures).

• Load the individual subject surfaces (e.g. lh.white, lh.pial) along with the T1 or brain volumes to be able to assess the quality of the surface reconstruction.

• Load for an individual subject load both a main and an auxilliary surface overlaid on the same volume (e.g. to compare the results of two different reconstruction algorithms)- e.g. two lh.white where each is indicated by a different color) requested by Xiao.

• Load along with the surface, the cortical parcellation maps (lh.aparc.annot), to view these results.

• For group average results, be able to load the average surface (lh or rh) and the corresponding t-statxxxxx.w file overlay.

• Grand challenges: 1) do QA of a data set that has been been through the subcortical segmentation and cortical parcellation algorithms. 2) Prepare figure for publication of the results of a group analysis of cortical thickness using the Freesurfer tutorial example 3) Prepare figure for publication of the hippocampal models from bert, where the right and left hippocampi are viewed over the brain volume, with the top of the brain cut off to see them looking down from above.

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