[Freesurfer] autorecon2
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[EMAIL PROTECTED] EM Registration Mon May 1 12:06:14 EDT 2006[EMAIL PROTECTED] CA Normalize Mon May 1 12:13:52 EDT 2006[EMAIL PROTECTED] CA Reg Mon May 1 12:16:45 EDT 2006[EMAIL PROTECTED] CA Reg Inv Mon May 1 20:26:29 EDT 2006 [EMAIL PROTECTED] Remove Neck Mon May 1 20:29:30 EDT 2006[EMAIL PROTECTED] SkullLTA Mon May 1 20:33:45 EDT 2006[EMAIL PROTECTED] SubCort Seg Mon May 1 20:45:47 EDT 2006[EMAIL PROTECTED] ASeg Stats Mon May 1 21:35:30 EDT 2006[EMAIL PROTECTED] Intensity Normalization2 Mon May 1 22:00:03 EDT 2006 [EMAIL PROTECTED] Mask BFS Mon May 1 22:10:28 EDT 2006[EMAIL PROTECTED] WM Segmentation Mon May 1 22:10:41 EDT 2006[EMAIL PROTECTED] Fill Mon May 1 22:19:24 EDT 2006[EMAIL PROTECTED] Tessellate lh Mon May 1 22:23:00 EDT 2006[EMAIL PROTECTED] Smooth1 lh Mon May 1 22:23:11 EDT 2006 [EMAIL PROTECTED] Inflation1 lh Mon May 1 22:23:27 EDT 2006[EMAIL PROTECTED] QSphere lh Mon May 1 22:27:12 EDT 2006[EMAIL PROTECTED] Fix Topology lh Mon May 1 22:53:31 EDT 2006[EMAIL PROTECTED] Make Final Surf lh Tue May 2 04:36:31 EDT 2006\n\nNew invocation of recon-all \n\nstatus file for recon-allTue May 2 10:17:17 EDT 2006[EMAIL PROTECTED] Sphere lh Tue May 2 10:17:17 EDT 2006Darwin 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 powerpcrecon-all exited with ERRORS at Tue May 2 10:17:17 EDT 2006 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] autorecon2
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 [EMAIL PROTECTED] EM Registration Mon May 1 12:06:14 EDT 2006 [EMAIL PROTECTED] CA Normalize Mon May 1 12:13:52 EDT 2006 [EMAIL PROTECTED] CA Reg Mon May 1 12:16:45 EDT 2006 [EMAIL PROTECTED] CA Reg Inv Mon May 1 20:26:29 EDT 2006 [EMAIL PROTECTED] Remove Neck Mon May 1 20:29:30 EDT 2006 [EMAIL PROTECTED] SkullLTA Mon May 1 20:33:45 EDT 2006 [EMAIL PROTECTED] SubCort Seg Mon May 1 20:45:47 EDT 2006 [EMAIL PROTECTED] ASeg Stats Mon May 1 21:35:30 EDT 2006 [EMAIL PROTECTED] Intensity Normalization2 Mon May 1 22:00:03 EDT 2006 [EMAIL PROTECTED] Mask BFS Mon May 1 22:10:28 EDT 2006 [EMAIL PROTECTED] WM Segmentation Mon May 1 22:10:41 EDT 2006 [EMAIL PROTECTED] Fill Mon May 1 22:19:24 EDT 2006 [EMAIL PROTECTED] Tessellate lh Mon May 1 22:23:00 EDT 2006 [EMAIL PROTECTED] Smooth1 lh Mon May 1 22:23:11 EDT 2006 [EMAIL PROTECTED] Inflation1 lh Mon May 1 22:23:27 EDT 2006 [EMAIL PROTECTED] QSphere lh Mon May 1 22:27:12 EDT 2006 [EMAIL PROTECTED] Fix Topology lh Mon May 1 22:53:31 EDT 2006 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: MINC toolkit
Hi After having major hard drive problems i've lost the minc tools that i had installed at /usr/pubsw/packages/mni/current/lib so i need to download the minc tools again. I've been trying to download them from: https://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads but when i click on the link for MINC tools I get: "The requested URL /pub/dist/fs_supportlibs/mni-prebuilt/mni-1.4_rh9.tar.gz was not found on this server." Is there somewhere else I can get the tools from? I know they now come packaged with the full freesurfer program but I don't want to download the whole thing as I've downloaded 3 versions of freesurfer already! thanks! Jane -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: MINC toolkit
Hi Jane, Try: https://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/binaries/rh9/mni-1.4_rh9.tar.gz I'll go ahead and fix those links. Thanks, Dennis Jane Aspell wrote: Hi After having major hard drive problems i've lost the minc tools that i had installed at /usr/pubsw/packages/mni/current/lib so i need to download the minc tools again. I've been trying to download them from: https://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads but when i click on the link for MINC tools I get: "The requested URL /pub/dist/fs_supportlibs/mni-prebuilt/mni-1.4_rh9.tar.gz was not found on this server." Is there somewhere else I can get the tools from? I know they now come packaged with the full freesurfer program but I don't want to download the whole thing as I've downloaded 3 versions of freesurfer already! thanks! Jane ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Results files
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
Re: [Freesurfer] Results files
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: MINC toolkit
Sorry, broken link in the wiki (fixed now). Use: https://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/binaries/rh9/mni-1.4_rh9.tar.gz > Hi > > After having major hard drive problems i've lost the minc tools that i had > installed at /usr/pubsw/packages/mni/current/lib so i need to download > the minc > tools again. I've been trying to download them from: > > https://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads > > but when i click on the link for MINC tools I get: > > "The requested URL > /pub/dist/fs_supportlibs/mni-prebuilt/mni-1.4_rh9.tar.gz was > not found on this server." > > Is there somewhere else I can get the tools from? I know they now come > packaged > with the full freesurfer program but I don't want to download the whole > thing as > I've downloaded 3 versions of freesurfer already! > > thanks! > > Jane > > > -- > Dr Jane Aspell > Department of Experimental Psychology, University of Oxford, > South Parks Road, Oxford, OX1 3UD > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] libtiff 3 or 4?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I'm wondering what the current version of libtiff is at on redhat systems. I only see the following for Debian systems at: http://packages.debian.org/cgi-bin/search_packages.pl?keywords=libtiff&searchon=names&subword=1&version=stable&release=all You have searched for packages that names contain libtiff in suite(s) stable, all sections, and all architectures. Found 5 matching packages, displaying packages 1 to 5. Package libtiff-opengl * stable (graphics): TIFF manipulation and conversion tools 3.7.2-3: alpha amd64 arm hppa i386 ia64 mips mipsel powerpc s390 sparc Package libtiff-tools * stable (graphics): TIFF manipulation and conversion tools 3.7.2-3: alpha amd64 arm hppa i386 ia64 mips mipsel powerpc s390 sparc Package libtiff4 * stable (libs): Tag Image File Format (TIFF) library 3.7.2-3: alpha amd64 arm hppa i386 ia64 mips mipsel powerpc s390 sparc Package libtiff4-dev * stable (libdevel): Tag Image File Format library (TIFF), development files 3.7.2-3: alpha amd64 arm hppa i386 ia64 mips mipsel powerpc s390 sparc Package libtiffxx0 * stable (libs): Tag Image File Format (TIFF) library -- C++ interface 3.7.2-3: alpha amd64 arm hppa i386 ia64 mips mipsel powerpc s390 sparc - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFEV/dVxaCYN7qs0v4RAgxJAKCXlJ9i0EjXmsQsoCrndHg44DAfRACfXxQM PZ8BMV2FzPo/wEMKX8OTk2U= =ePfK -END PGP SIGNATURE- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
