Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

fill stats
by Chris Baker 04 May '06

04 May '06

Hi, Is there a way when using 'fill stats' to only select either the positive or negative values rather than taking both? Cheers, Chris.

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Fwd: [Freesurfer] buying computer - machine requirements
by Jacek Jonca-Jasinki 04 May '06

04 May '06

Kayle, > 1. HDD speed: How hard disk (I/O speed) intensive is freesurfer? What kind of > speed difference will having a RAID make? Would there be a big difference > from plain SATA? Gererally RAID would be most beneficial for computers running large number of search and read operations (i.e. database queries in large databases) as it requires number of rapid movements across large surface of the disk and there are some constraints of how quickly search and read can happen. That is one of the reasons why people use raid arrays. However, I doubt if in your case you will see much of the difference in performance. However, I would consider having two RAID mirrored drives that will impove security of you data. In case one of the drives fails some or all data from the other drive can be recovered preventing data loss. > 2. RAM amount: How much memory does running recon-all for one subject generally > require? Is it 0.5-1.5GB? Would 2GB be enough to run two simultaneously or do I > need 4GB? Or 6GB? How much RAM does running a group map for functionals need? Standard seems to be 4GB you may be able to get away with 2GB and I would not recommend less than that. Please note that those are only my wild guesses. > 3. RAM speed: We are buying DDR400 PC3200 RAM. Should I bother paying more for low-latency timings? Don't bother paying for faster memory, your bottleneck is your harddrive not your memory. > 4. Graphics speed: What speed graphics card is good enough for tkmedit and > tksurfer? Is a Geforce 6000 series plenty, or does having a 7000 series make > any difference? See this website for benchmarks of videocards: http://www.tomshardware.com/site/vgacharts/index.html -jacek

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buying computer - machine requirements
by kslays＠bu.edu 04 May '06

04 May '06

Hi, My group is buying a new computer we will use in the Martinos Center. I emailed Paul Raines via help and he gave me some guidelines as to what type I should get, but I still have some questions. 1. HDD speed: How hard disk (I/O speed) intensive is freesurfer? What kind of speed difference will having a RAID make? Would there be a big difference from plain SATA? 2. RAM amount: How much memory does running recon-all for one subject generally require? Is it 0.5-1.5GB? Would 2GB be enough to run two simultaneously or do I need 4GB? Or 6GB? How much RAM does running a group map for functionals need? 3. RAM speed: We are buying DDR400 PC3200 RAM. Should I bother paying more for low-latency timings? 4. Graphics speed: What speed graphics card is good enough for tkmedit and tksurfer? Is a Geforce 6000 series plenty, or does having a 7000 series make any difference? 5. Has anyone tried clustering computers together to spread the processing? Should we look into this for our three P4 1Ghz machines? Maybe you could add this information to the Machine Requirements wiki pages? https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements Thanks, Kayle

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mri_convert: input filetype = nrrd
by Michael Rullmann 04 May '06

04 May '06

hey, i tried to convert a nrrd file to mgz. but i didn't work because mri_convert doesn't support the nrrd filetype. is there any chance to use nrrd as a input file for freesurfer? does anyone knows a converter which converts nrrd files to analyze/dicom/... ? thanks, michael.

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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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