Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

recon-all - skip motion correction
by Darren Weber 03 May '06

03 May '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, we have only 1 orig.mgz file, so motion correction is not required. In this case, it would be ideal if recon-all auto-detected or at least had an option to skip motion correction. As it is, it fails entirely when no 001.mgz file exists. I have a file called orig.mgz, should it be renamed to 001.mgz even though there is no 002.mgz? endorphin.32> ls -l ucsf_disc01/mri/orig/ total 5784 - -rw-rw-rw- 1 dweber dnl 5907576 May 3 13:52 orig.mgz endorphin.31> recon-all -subjid ucsf_disc01 -all INFO: SUBJECTS_DIR is /data/dnl-raid2/freesurfer/subjects Actual FREESURFER_HOME /data/dnl-raid1/freesurfer - -rw-rw---- 1 dweber dnl 56553 May 3 13:55 /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/scripts/recon-all.log Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux WM removal version #-------------------------------------------- #@# MotionCor Wed May 3 13:55:54 PDT 2006 ERROR: no run data found in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri. Make sure to have a volume called 001.mgz in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed May 3 13:55:54 PDT 2006 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 iD8DBQFEWRnuxaCYN7qs0v4RAo91AKCisc5QNJhVDGySLbhZivaA/TBwjACeNuLs i71i+loDc67uAvWeHV37NzA= =eoyz -----END PGP SIGNATURE-----

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registration problems
by Chris Baker 03 May '06

03 May '06

Hi, I'm trying to register a set of functionals with anatomical data and am finding that even though the registration looks good when viewed in tkregister (see snapshot below), when I look at the data in tkmedit or tksurfer, the alignment is completely off (see second snapshot). It looks almost as if the size of the functional slab is being read incorrectly with respect to the anatomicals, although all the information in register.dat looks OK (see below). Any ideas how to fix this or what the problem is? Could this be a problem with paint-sess or surf-sess. I'm using versions $Id: paint-sess,v 1.9 2006/01/09 23:44:42 greve Exp $ $Id: surf-sess,v 1.12 2005/08/30 16:56:04 greve Exp $ Thanks for any help, Chris. filling-in001 3.000000 3.300000 0.100000 9.998358e-01 -8.742601e-04 7.647049e-04 8.429348e-01 -6.269891e-04 6.565273e-01 7.541288e-01 4.779076e+01 9.408451e-04 7.537801e-01 -6.573987e-01 2.930424e+01 5.640810e-12 8.807770e-12 -1.513114e-12 1.000000e+00 round

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Re: [Freesurfer] Re: mk-fieldsign problems
by Jane Aspell 03 May '06

03 May '06

Hi I would be really grateful if someone could help me with the problems I am having with mk-fieldsign. Even after installing a new version of freesurfer and making various changes to libraries etc. when i run: "paint-sess -sf sessid -a rtopy -hemi rh" i get the error below: tksurfer: run tcl script: mk-fieldsign.tcl couldn't read file "mk-fieldsign.tcl": no such file or directory even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which works fine). i am running Red Hat Linux release 9 (Shrike) and installed from freesurfer-Linux-rh9-v2.2.tar.gz any idea what to do? thanks again for your help! Jane In message <1134599450.17318.34.camel(a)minerva.nmr.mgh.harvard.edu> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> writes: > Jane, > > Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does > not use these libraries any more (I think the older -20040218 release > did, however). > > Do you have the environment variable ITCL_LIBRARY defined in your > startup .cshrc file? You can test if it is set by typing (in csh or > tcsh): > > env|grep ITCL > > If it is set (which it might be, from your older freesurfer > installation), then it should be deleted or commented-out from > your .cshrc (or possibly it was placed in your > $FREESURFER_HOME/SetUpFreeSurfer.csh file). > > You can also just type this: > > unsetenv ITCL_LIBRARY > > and then try tkmedit. > > If this is not the problem, can you tell me which OS you are running? > Type: > > cat /etc/redhat-release > > and > > uname -a > > A last ditch effort is to install the itcl libs, from this site: > > http://rpmfind.net/linux/rpm2html/search.php?query=itcl > > But this should not be necessary, as tkmedit that you have does not use > this library (I am truly puzzled why 'ldd' shows that it needs these > libs). > > Thanks, > > Nick > > > On Mon, 2005-12-12 at 11:40 +0000, Jane Aspell wrote: > > hi nick > > > > when i type >ldd `which tkmedit` i get the ouput pasted below this email. > > libitk3.2.so and libitcl3.2.so are not found - could be the problem? > > > > uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh > > (and typing 'unsetenv TCLLIBPATH') had no effect. > > > > an earlier version of freesurfer(freesurfer-20040218) didn't give me any of > > these problems and tkmedit etc worked fine. > > > > also, does ANYONE know how to interpret the colour coding (for fovea/vertical > > meridian etc) produced by the FsFast retinotopy analysis?! > > > > thanks again! > > > > jane > > > > > > >ldd `which tkmedit` > > libtix8.1.8.3.so => > > /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000) > > libtk8.4.so => /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so > > (0x40051000) > > libtcl8.4.so => > > /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000) > > libglut.so.3 => /usr/lib/libglut.so.3 (0x401ba000) > > libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401ef000) > > libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401f8000) > > libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x40210000) > > libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000) > > libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000) > > libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x402ab000) > > libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x402ef000) > > libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x403ce000) > > libtiff.so.3 => /usr/lib/libtiff.so.3 (0x403ed000) > > libcrypt.so.1 => /lib/libcrypt.so.1 (0x4042e000) > > libz.so.1 => /usr/lib/libz.so.1 (0x4045b000) > > libm.so.6 => /lib/tls/libm.so.6 (0x40469000) > > libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4048b000) > > libc.so.6 => /lib/tls/libc.so.6 (0x42000000) > > libitk3.2.so => not found > > libitcl3.2.so => not found > > libdl.so.2 => /lib/libdl.so.2 (0x4049a000) > > libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x4049e000) > > libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x404f0000) > > libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x404ff000) > > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x405b2000) > > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) > > > > > > > > In message <1133802940.21136.14.camel(a)minerva.nmr.mgh.harvard.edu> Nick > > Schmansky <nicks(a)nmr.mgh.harvard.edu> writes: > > > Jane, > > > > > > This is an unusual error, since tkmedit and tksurfer do not use the ITK > > > library. To figure out how libitk3.2.so is being referenced, can you > > > send me the output of this command: > > > > > > ldd `which tkmedit` > > > > > > I suspect there is some conflict between the FSL setup and Freesurfer, > > > as FSL does use ITK, and Freesurfer does not, but performs the FSL setup > > > (as a convenience to MGH-NMR users). Along this line, one option is to > > > edit the file FreeSurferEnv.csh (found in your $FREESURFER_HOME) and > > > comment-out this line: > > > > > > source ${FSL_DIR}/etc/fslconf/fsl.csh > > > > > > like this: > > > > > > # source ${FSL_DIR}/etc/fslconf/fsl.csh > > > > > > Another option is to type this after sourcing the freesurfer setup file: > > > > > > unsetenv TCLLIBPATH > > > > > > This last option is just a guess at a fix though. > > > > > > Nick > > > > > > > > > On Mon, 2005-12-05 at 15:37 +0000, Jane Aspell wrote: > > > > hi > > > > > > > > i installed a newer version of freesurfer (using download > > > > freesurfer-Linux-rh9-v2.2.tar.gz) but when i try and run tkmedit or tksurfer i > > > > get the error: > > > > > > > > "error while loading shared libraries: libitk3.2.so: cannot open shared object > > > > file: No such file or directory" > > > > > > > > this is my output when i source SetUpFreeSurfer.csh: > > > > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > FREESURFER_HOME /home/jaspell/freesurfer > > > > FSFAST_HOME /home/jaspell/freesurfer/fsfast > > > > SUBJECTS_DIR /home/jaspell/freesurfer/subjects > > > > FUNCTIONALS_DIR /home/jaspell/freesurfer/sessions > > > > MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin > > > > MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib > > > > TCLLIBPATH /home/jaspell/freesurfer/lib/tcltktixblt/lib > > > > FSL_DIR /usr/local/fsl > > > > > > > > and these are the contents of /home/jaspell/freesurfer/lib/tcltktixblt/lib: > > > > > > > > blt2.4/ libBLTlite24.a libtclstub8.4.a libtk8.4.so* > > > > tix8.1/ > > > > libBLT24.a* libBLTlite.2.4.dylib* libtix8.1.8.3.so libtk.so.0* > > > > tixConfig.sh > > > > libBLT.2.4.dylib* libBLTlite.a libtix8.1.8.4.so libtkstub8.4.a > > > > tk8.4/ > > > > libBLT.2.dylib* libtcl8.4.so* libtixsam8.1.8.4.so tcl8.4/ > > > > tkConfig.sh > > > > libBLT.a* libtcl.so.0* libtix.so.0 tclConfig.sh > > > > > > > > > > > > any idea how to fix it? > > > > > > > > i don't suppose there's a way of updating an old version of freesurfer without > > > > reinstalling the entire (new version) package? > > > > > > > > thanks! > > > > > > > > jane > > > > > > > > > > > > > > > > > > > > In message <Pine.LNX.4.62.0512021326490.5676(a)icebox.nmr.mgh.harvard.edu> Doug > > > > Greve <greve(a)nmr.mgh.harvard.edu> writes: > > > > > > > > > > That's a pretty old version. Can you download and install a new version? > > > > > > > > > > I actually don't know that much about the interpretation of the color > > > > > wheel. Maybe Nouchine or Sari can help with this. > > > > > > > > > > doug > > > > > > > > > > > > > > > On Fri, 2 Dec 2005, Jane Aspell wrote: > > > > > > > > > > > hi again > > > > > > > > > > > > i'm still really stuck with my retinotopy analysis as i'm not sure if my > > > > > > version of paint-sess $Id: paint-sess,v 1.2 2003/08/06 00:53:50 greve Exp $ > > > > > > FAST Version 20031218) has a bug in it (it doesn't make the field sign > > map). i > > > > > > originally downloaded freesurfer-20040218-Linux.tar.gz (for RedHat 9). > > > > > > > > > > > > also, can someone also confrim the colour coding is: red=upper field/fovea, > > > > > > blue=horizontal meridian/parafovea, green=lower visual field/periphery? > > > > > > > > > > > > i can't work out what the overlay threshold settings should be in > > tksurfer to > > > > > > correctly display the colours to code the retinotopy, is there some > > rationale > > > > > > for choosing them? > > > > > > > > > > > > thanks a lot for your help! > > > > > > > > > > > > Jane > > > > > > > > > > > > > > > > > > In message > > <Pine.LNX.4.62.0511280225500.19611(a)icebox.nmr.mgh.harvard.edu> Doug > > > > > > Greve <greve(a)nmr.mgh.harvard.edu> writes: > > > > > >> > > > > > >> What version of freesurfer (and paint-sess) are you using? This was a > > > > > >> problem in some versions about 6 mo ago, but I thought I fixed them > > > > > >> all. > > > > > >> > > > > > >> doug > > > > > >> > > > > > >> > > > > > >> > > > > > >> On Thu, 24 Nov 2005, Jane Aspell wrote: > > > > > >> > > > > > >>> hi again > > > > > >>> I have been proceeding with the retinotopy analysis using FsFast, > > > > > > following the > > > > > >>> instructions at: > > > > > >>> > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > > > > > >>> and i believe i have successfully overlaid the results on my surfaces and > > > > > > now > > > > > >>> have two questions: > > > > > >>> > > > > > >>> i wasn't able to create the fieldsign with 'paint-sess' because it > > > > > > couldn't find > > > > > >>> tksurfer.new. when i run 'surf-sess' i use the flag -old which forces it > > > > > > to use > > > > > >>> tksurfer.old but this doesn't work in the former case. how can i make > > > > > >>> 'paint-sess' use tksurfer.old and thus create the fieldsign? > > > > > >>> > > > > > >>> there are no instructions on how to relate the colours seen when viewing > > > > > > eccen > > > > > >>> and polar to the location of the ring and wedge. is there a map somewhere > > > > > > that > > > > > >>> can be loaded that tells me what order the colours run from fovea to > > > > > > periphery > > > > > >>> and from vertical to horizontal meridian etc.? > > > > > >>> > > > > > >>> thanks again for your help! > > > > > >>> > > > > > >>> jane > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >> > > > > > >> -- > > > > > >> Douglas N. Greve, Ph.D. > > > > > >> MGH-NMR Center > > > > > >> greve(a)nmr.mgh.harvard.edu > > > > > >> Phone Number: 617-724-2358 > > > > > >> Fax: 617-726-7422 > > > > > >> > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > >

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libtiff 3 or 4?
by Darren Weber 02 May '06

02 May '06

-----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&sear… 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-----

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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

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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-----

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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

Skullstripping
by Joao Pereira 29 Apr '06

29 Apr '06

Can someone explain me why my the recon-all skull stripping option is writting a file named brainmask.mgz instead of brain.mgz? This is a problem because the subsequent procedures do not recognize the file. Thank you! JP

3 4

Surface intersections
by rhaynes＠neuro.gatech.edu 28 Apr '06

28 Apr '06

After running the final processing stage of recon-all, I viewed the results in tkmedit and noticed several places where the wm and pial surfaces intersect (see attachment). This mostly happens on the medial and temporal areas, but I have seen it elsewhere. Doesn't this cause problems with the cortical thickness estimation? Is there anything else I should be doing to correct this? Thanks. Ryan

2 1

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