Dear freesurferers,
I have two questions about the recon-all with -autorecon2 option.
First one is about ASeg Stats (mri_segstats). In the following status log, I found that ASeg Stats step was executed as a final step of -autorecon2:
status file for recon-all Sat Mar 16 21:50:42 JST 2013 #@# EM Registration Sat Mar 16 21:50:42 JST 2013 #@# CA Normalize Sat Mar 16 22:13:19 JST 2013 #@# CA Reg Sat Mar 16 22:15:14 JST 2013 #@# CA Reg Inv Sun Mar 17 01:57:37 JST 2013 #@# Remove Neck Sun Mar 17 01:58:47 JST 2013 #@# SkullLTA Sun Mar 17 02:00:06 JST 2013 #@# SubCort Seg Sun Mar 17 02:23:38 JST 2013 #@# Merge ASeg Sun Mar 17 02:50:50 JST 2013 #@# Intensity Normalization2 Sun Mar 17 02:50:50 JST 2013 #@# Mask BFS Sun Mar 17 02:54:56 JST 2013 #@# WM Segmentation Sun Mar 17 02:54:58 JST 2013 #@# Fill Sun Mar 17 02:57:59 JST 2013 #@# Tessellate lh Sun Mar 17 02:58:54 JST 2013 #@# Smooth1 lh Sun Mar 17 02:59:01 JST 2013 #@# Inflation1 lh Sun Mar 17 02:59:04 JST 2013 #@# QSphere lh Sun Mar 17 02:59:28 JST 2013 #@# Fix Topology lh Sun Mar 17 03:02:37 JST 2013 #@# Make White Surf lh Sun Mar 17 03:23:10 JST 2013 #@# Smooth2 lh Sun Mar 17 03:33:13 JST 2013 #@# Inflation2 lh Sun Mar 17 03:33:17 JST 2013 #@# Curvature Stats lh Sun Mar 17 03:35:12 JST 2013 #@# Tessellate rh Sun Mar 17 03:35:17 JST 2013 #@# Smooth1 rh Sun Mar 17 03:35:23 JST 2013 #@# Inflation1 rh Sun Mar 17 03:35:26 JST 2013 #@# QSphere rh Sun Mar 17 03:35:50 JST 2013 #@# Fix Topology rh Sun Mar 17 03:39:04 JST 2013 #@# Make White Surf rh Sun Mar 17 03:56:40 JST 2013 #@# Smooth2 rh Sun Mar 17 04:06:43 JST 2013 #@# Inflation2 rh Sun Mar 17 04:06:46 JST 2013 #@# Curvature Stats rh Sun Mar 17 04:08:41 JST 2013 #@# ASeg Stats Sun Mar 17 04:08:46 JST 2013 recon-all -s bert finished without error at Sun Mar 17 04:11:54 JST 2013
According to the help document for recon-all, ASeg Stats should run in the -autorecon3 step, not in -autorecon2. Is this some kind of bug? http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1?action=prin...
Second questions is about Cortical Ribbon Mask. At the Manual-Intervention Workflow Directives in recon-all help, Cortical Ribbon Mask is classified into the part of -autorecon3. However, the Step Description Summaries says that the -autorecon2 stage ends at the Cortical Ribbon Mask. Which one is right? http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Thanks, Hiroki