I was running autorecon2 and it did not finish. The status.log file tells me that it is finished but the data does not appear in the surf folder (some of the lh data is there but no rh). Here is the end of the log file......does that help? I tried to run autorecon3 and that was the "new invocation". I am just not sure why the right hemisphere didn't finish. Is there a command to tell the program to start after "make Final Surf lh"??? Thanks for your consideration.
Mon May 1 12:06:14 EDT 2006 #@# EM Registration Mon May 1 12:06:14 EDT 2006 #@# CA Normalize Mon May 1 12:13:52 EDT 2006 #@# CA Reg Mon May 1 12:16:45 EDT 2006 #@# CA Reg Inv Mon May 1 20:26:29 EDT 2006 #@# Remove Neck Mon May 1 20:29:30 EDT 2006 #@# SkullLTA Mon May 1 20:33:45 EDT 2006 #@# SubCort Seg Mon May 1 20:45:47 EDT 2006 #@# ASeg Stats Mon May 1 21:35:30 EDT 2006 #@# Intensity Normalization2 Mon May 1 22:00:03 EDT 2006 #@# Mask BFS Mon May 1 22:10:28 EDT 2006 #@# WM Segmentation Mon May 1 22:10:41 EDT 2006 #@# Fill Mon May 1 22:19:24 EDT 2006 #@# Tessellate lh Mon May 1 22:23:00 EDT 2006 #@# Smooth1 lh Mon May 1 22:23:11 EDT 2006 #@# Inflation1 lh Mon May 1 22:23:27 EDT 2006 #@# QSphere lh Mon May 1 22:27:12 EDT 2006 #@# Fix Topology lh Mon May 1 22:53:31 EDT 2006 #@# Make Final Surf lh Tue May 2 04:36:31 EDT 2006 \n\n New invocation of recon-all \n\n status file for recon-all Tue May 2 10:17:17 EDT 2006 #@# Sphere lh Tue May 2 10:17:17 EDT 2006 Darwin Pterodactyl.local 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc
recon-all exited with ERRORS at Tue May 2 10:17:17 EDT 2006
Hi Anthony,
it says that it finsiehd with errors. Can you see what the error was in the log file?
Bruce
On Tue, 2 May 2006, anthony gallo wrote:
I was running autorecon2 and it did not finish. The status.log file tells me that it is finished but the data does not appear in the surf folder (some of the lh data is there but no rh). Here is the end of the log file......does that help? I tried to run autorecon3 and that was the "new invocation". I am just not sure why the right hemisphere didn't finish. Is there a command to tell the program to start after "make Final Surf lh"??? Thanks for your consideration.
Mon May 1 12:06:14 EDT 2006 #@# EM Registration Mon May 1 12:06:14 EDT 2006 #@# CA Normalize Mon May 1 12:13:52 EDT 2006 #@# CA Reg Mon May 1 12:16:45 EDT 2006 #@# CA Reg Inv Mon May 1 20:26:29 EDT 2006 #@# Remove Neck Mon May 1 20:29:30 EDT 2006 #@# SkullLTA Mon May 1 20:33:45 EDT 2006 #@# SubCort Seg Mon May 1 20:45:47 EDT 2006 #@# ASeg Stats Mon May 1 21:35:30 EDT 2006 #@# Intensity Normalization2 Mon May 1 22:00:03 EDT 2006 #@# Mask BFS Mon May 1 22:10:28 EDT 2006 #@# WM Segmentation Mon May 1 22:10:41 EDT 2006 #@# Fill Mon May 1 22:19:24 EDT 2006 #@# Tessellate lh Mon May 1 22:23:00 EDT 2006 #@# Smooth1 lh Mon May 1 22:23:11 EDT 2006 #@# Inflation1 lh Mon May 1 22:23:27 EDT 2006 #@# QSphere lh Mon May 1 22:27:12 EDT 2006 #@# Fix Topology lh Mon May 1 22:53:31 EDT 2006 #@# Make Final Surf lh Tue May 2 04:36:31 EDT 2006 \n\n New invocation of recon-all \n\n status file for recon-all Tue May 2 10:17:17 EDT 2006 #@# Sphere lh Tue May 2 10:17:17 EDT 2006 Darwin Pterodactyl.local 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc
recon-all exited with ERRORS at Tue May 2 10:17:17 EDT 2006
Dear All: I am using the last relaease of freesurefr and I am uncertain about the '.aparc.stats' file. Precisly: differences between this file and the '.aparc.a2005s.stats' and '.aparc.stats' are not clear. Does the latter selecet dome of the cortical regions form the first one? If so, avg thick of similar regions does not look to coincide according to the numbers I got. Just wondering...
Thanks for your help. Francesca
Hi Francesca,
Freesurfer now runs two parcellations, by default. One (?h.aparc.annot) uses the Desikan-Killiany atlas and the other (?h.aparc.a2005s.annot) uses Christophe's atlas. The two stat files are the different statistical outputs that come from each of the different atlases.
Jenni
On Tue, 2 May 2006, Bagnato, Francesca (NIH/NINDS) [E] wrote:
Dear All: I am using the last relaease of freesurefr and I am uncertain about the '.aparc.stats' file. Precisly: differences between this file and the '.aparc.a2005s.stats' and '.aparc.stats' are not clear. Does the latter selecet dome of the cortical regions form the first one? If so, avg thick of similar regions does not look to coincide according to the numbers I got. Just wondering...
Thanks for your help. Francesca
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
anthony gallo -
Bagnato, Francesca (NIH/NINDS) [E] -
Bruce Fischl -
Jenni Pacheco