Freesurfer May 2006

freesurfer@nmr.mgh.harvard.edu

50 participants
74 discussions

autorecon2
by anthony gallo 02 May '06

02 May '06

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

4 3

GNU GPL source?
by Darren Weber 01 May '06

01 May '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Bruce et al., I don't see the GNU source download on the wiki. Have you withdrawn that download? I have a Debian testing (etch) system, running in UNICODE mode. The rh9 version of tksurfer requires libtiff3, but libtiff4 is now available, ie: dnlweber:~/bin/cpp> ls -l /usr/lib/libtiff* - -rw-r--r-- 1 root root 412842 2006-03-28 18:49 /usr/lib/libtiff.a - -rw-r--r-- 1 root root 971 2006-03-28 18:49 /usr/lib/libtiff.la lrwxrwxrwx 1 root root 16 2006-04-19 23:30 /usr/lib/libtiff.so -> libtiff.so.4.2.1 lrwxrwxrwx 1 root root 16 2006-04-17 16:38 /usr/lib/libtiff.so.4 -> libtiff.so.4.2.1 - -rw-r--r-- 1 root root 341988 2006-03-28 18:49 /usr/lib/libtiff.so.4.2.1 - -rw-r--r-- 1 root root 6322 2006-03-28 18:49 /usr/lib/libtiffxx.a - -rw-r--r-- 1 root root 997 2006-03-28 18:49 /usr/lib/libtiffxx.la lrwxrwxrwx 1 root root 18 2006-04-19 23:30 /usr/lib/libtiffxx.so -> libtiffxx.so.0.0.6 lrwxrwxrwx 1 root root 18 2006-04-19 23:30 /usr/lib/libtiffxx.so.0 - -> libtiffxx.so.0.0.6 - -rw-r--r-- 1 root root 7528 2006-03-28 18:49 /usr/lib/libtiffxx.so.0.0.6 Anyhow, I'm interested in compiling freesurfer. I recall there was a download and instructions for this. Thanks, Darren - -- 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 iD8DBQFEViSOxaCYN7qs0v4RAss0AJ0RWUQmcWzxntNrexGtnSSOPQGC8wCfcfn1 Kc7NW/rZrZdK3zrkhWRcKHI= =jXET -----END PGP SIGNATURE-----

3 4

RE: [Freesurfer] GNU GPL source?
by Kirk, Gregory 01 May '06

01 May '06

It would be nice whatever could be available for having a detailed look At what some of the code does. Also for persons anticipating trying To do some algorithm work a bit of perusing the code to having a working Understanding would be interesting. Also maybe feedback on what parts of the Code are most in need of a bit of explaining might help with allocating the limited Amount of resources you will be able to devote to such efforts. Cheerio Greg. -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, May 01, 2006 1:02 PM To: Nick Schmansky Cc: Darren.Weber(a)radiology.ucsf.edu; Freesurfer Mailing List Subject: Re: [Freesurfer] GNU GPL source? p.s. we can't use GPL because of various MGH restrictions (which also unfortunately means we can't use any other GPL code). We could conceivably post an incomplete (and thus unbuildable version) - would that be helpful? We're working towards a make/configure type open source, but aren't there yet. cheers, Bruce On Mon, 1 May 2006, Nick Schmansky wrote: > Darren, > > The freesurfer source code is not ready to be posted for download just > yet. We are currently replacing some code that we cannot distribute > as open-source. > > About your problem with libtiff, I suppose a hacky solution is to try > symlinking libtiff.so.3 to libtiff.so.4. I'll also check if we have a > Debian build on our network. > > Maybe you can answer a question for me. Do you know how to make an > application build against the .so library, instead of the .so.# > version? In other words, I don't know why our build chooses to build > against libtiff.so.3 instead of libtiff.so, since we don't rely on > anything special in the tiff library. > > Nick > > > > On Mon, 2006-05-01 at 08:09 -0700, Darren Weber wrote: >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Dear Bruce et al., >> >> I don't see the GNU source download on the wiki. Have you withdrawn >> that download? >> >> I have a Debian testing (etch) system, running in UNICODE mode. The >> rh9 version of tksurfer requires libtiff3, but libtiff4 is now >> available, ie: >> >> dnlweber:~/bin/cpp> ls -l /usr/lib/libtiff* >> - -rw-r--r-- 1 root root 412842 2006-03-28 18:49 /usr/lib/libtiff.a >> - -rw-r--r-- 1 root root 971 2006-03-28 18:49 /usr/lib/libtiff.la >> lrwxrwxrwx 1 root root 16 2006-04-19 23:30 /usr/lib/libtiff.so -> >> libtiff.so.4.2.1 >> lrwxrwxrwx 1 root root 16 2006-04-17 16:38 /usr/lib/libtiff.so.4 -> >> libtiff.so.4.2.1 >> - -rw-r--r-- 1 root root 341988 2006-03-28 18:49 /usr/lib/libtiff.so.4.2.1 >> - -rw-r--r-- 1 root root 6322 2006-03-28 18:49 /usr/lib/libtiffxx.a >> - -rw-r--r-- 1 root root 997 2006-03-28 18:49 /usr/lib/libtiffxx.la >> lrwxrwxrwx 1 root root 18 2006-04-19 23:30 /usr/lib/libtiffxx.so -> >> libtiffxx.so.0.0.6 >> lrwxrwxrwx 1 root root 18 2006-04-19 23:30 /usr/lib/libtiffxx.so.0 >> - -> libtiffxx.so.0.0.6 >> - -rw-r--r-- 1 root root 7528 2006-03-28 18:49 /usr/lib/libtiffxx.so.0.0.6 >> >> >> Anyhow, I'm interested in compiling freesurfer. I recall there was a >> download and instructions for this. >> >> Thanks, Darren >> >> >> - -- >> >> 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 >> >> iD8DBQFEViSOxaCYN7qs0v4RAss0AJ0RWUQmcWzxntNrexGtnSSOPQGC8wCfcfn1 >> Kc7NW/rZrZdK3zrkhWRcKHI= >> =jXET >> -----END PGP SIGNATURE----- >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

3T problems
by Fornito, Alexander 30 Apr '06

30 Apr '06

Hi, I'm trying to segment some Siemens 3T images (200x200x256; 1mm3) and have encountered some problems at autorecon1 - the normalization seems to label some of the background as white matter. Needless to say, the skullstrip fails spectacularly. I've attached a snapshot of the T1 image showing the problem.Any ideas as to why this might occur? I'm running recon-all version 1.104 Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

4 5

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer May 2006