Freesurfer

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question
by Wan Park 23 Dec '04

23 Dec '04

I want to calculate the gray matter volume in certain areas (eg. cortical area 39). What should I do? Thanks, Wan

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mni_perllib_0.07 installation error
by Joongnam Yang 23 Dec '04

23 Dec '04

Happy holidays for everyone! When I was installing mni_perllib_0.07, the following error messages keep popping out and at the end installation fails. batch: error parsing command-line arguments Error closing pipe to batch: at t/batch-1.t line 36 `batch' exited with non-zero status code: 256 at t/batch-1.t line 36 t/batch-1........NOK 14tail: .out29406: No such file or directory t/batch-1........NOK 16/usr/bin/getopt: invalid option -- J /usr/bin/getopt: invalid option -- Q /usr/bin/getopt: invalid option -- l /usr/bin/getopt: invalid option -- S /usr/bin/getopt: invalid option -- s /usr/bin/getopt: invalid option -- o /usr/bin/getopt: invalid option -- e batch: error parsing command-line arguments Error closing pipe to batch: at t/batch-1.t line 112 `batch' exited with non-zero status code: 256 at t/batch-1.t line 112 Would someone give me a clue on how to fix it? Nam.

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Re: [Freesurfer] wmfill error
by Joongnam Yang 23 Dec '04

23 Dec '04

Thanks Margaret, Is there a reference on how to specify the corpus collosum and pons in the WMFill under Preferences->Expert Preferences in csurf? Nam. >>> Margaret Duff <mduff(a)nmr.mgh.harvard.edu> 12/22/04 12:10 PM >>> i had this problem recently. try using recon-all -stage one in a terminal window instead of process volume in csurf. or specify the corpus collosum and pons in the WMFill tab under Preferences->Expert Preferences in csurf. it probably cant find where to segment. you might want to check the archives for more detail on this problem. hope this helps, margaret On Wed, 22 Dec 2004, Joongnam Yang wrote: > Hi all, > > During "create surface" on csurf, > right after "fill white matter" is done, as soon as "tesselate RH white > matter" starts, > an error message comes up, which is > > images filled: > somedirectory/mri/filled/COR-001...not found, wmfill first. > > I checked the directory of /mri/filled, which did not have COR-00* files. > There was only one file, COR-.info. > It seems that the first process in "create surface" (fill white matter) is > supposed to create all those COR-00* files in the /mri/filled, but none is > created. > I changed permission on the directory, to no avail. > Would someone suggest something? > > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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wmfill error
by Joongnam Yang 22 Dec '04

22 Dec '04

Hi all, During "create surface" on csurf, right after "fill white matter" is done, as soon as "tesselate RH white matter" starts, an error message comes up, which is images filled: somedirectory/mri/filled/COR-001...not found, wmfill first. I checked the directory of /mri/filled, which did not have COR-00* files. There was only one file, COR-.info. It seems that the first process in "create surface" (fill white matter) is supposed to create all those COR-00* files in the /mri/filled, but none is created. I changed permission on the directory, to no avail. Would someone suggest something? Nam.

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watershed values
by Goldman, Aaron (NIH/NIMH) 22 Dec '04

22 Dec '04

Hi, I'm trying to adjust the watershed thresholds on a few images, and have a question about the default watershed value. When I run the skullstrip without specifying a watershed value, the recon-all.log file typically says: preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent I'm guessing this means the program first tried a value of 25%, somehow determined it was too high, and then used a watershed threshold of 15% instead. Is this correct? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: <mailto:aarong@mail.nih.gov> aarong(a)mail.nih.gov

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recon-all -stage1 error
by Joongnam Yang 22 Dec '04

22 Dec '04

Hi all, I ran recon-all -stage1 -subjid ID with the following errors. Any comment woud be appreciated. ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source//minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.8 2002/08/05 00:53:50 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.11 2002/11/06 13:32:23 jason Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /diskc/NAM/DATADec04/DPJ --------------------------------------------- MotionCor Wed Dec 22 14:10:28 EST 2004 INFO: no runs were found in /diskc/NAM/DATADec04/DPJ/ANAT/mri/orig/XXX, however, there is a volume in /diskc/NAM/DATADec04/DPJ/ANAT/mri/orig, so I am just going to proceed with that as the input. --------------------------------------------- Talairach Wed Dec 22 14:10:31 EST 2004 /diskc/NAM/DATADec04/DPJ/ANAT/mri talairach2 ANAT INFO: registering ANAT Wed Dec 22 14:10:31 EST 2004 -------------------------------------------- mri_convert orig orig/orig.mnc mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "eng_US" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). defined(@array) is deprecated at /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. (Maybe you should just omit the defined()?) -------------------------------------------- mri_add_xform_to_header /diskc/NAM/DATADec04/DPJ/ANAT/mri/transforms/talairach.xfm /diskc/NAM/DATADec04/DPJ/ANAT/mri/orig /diskc/NAM/DATADec04/DPJ/ANAT/mri/orig Wed Dec 22 14:12:14 EST 2004 --------------------------------------------- Nu Intensity Correction Wed Dec 22 14:12:14 EST 2004 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "eng_US" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/local/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/mni/bin/nu_correct line 37. ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on /dev/hda7 54459572 26175492 25517692 51% /diskc ------------------------------------------ recon-all exited with errors at Wed Dec 22 14:12:24 EST 2004

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stage1 error
by Joongnam Yang 22 Dec '04

22 Dec '04

Hi, I got the following error message when I ran recon-all -stage1 -subjid ID Any comments appreciated. Nam. Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/local/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/mni/bin/nu_correct line 37. ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on /dev/hda7 54459572 26175492 25517692 51% /diskc ------------------------------------------ recon-all exited with errors at Wed Dec 22 14:12:24 EST 2004

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Problem running recon-all
by Damaraju, Eswar 22 Dec '04

22 Dec '04

Hello everyone, I have recently upgraded my OS from RedHat Linux 9 to RedHat Enterprise edition. After that, I'm getting the following error when I run : $ recon-all -sid xxxx -stage1 ####################################### INFO: SUBJECTS_DIR is /home/edamaraju/freesurfer/subjects --------------------------------------------- MotionCor Tue Dec 21 18:22:55 EST 2004 INFO: no runs were found in /home/edamaraju/freesurfer/subjects/eFMRI02/mri/orig/XXX, however, there is a volume in /home/edamaraju/freesurfer/subjects/eFMRI02/mri/orig, so I am just going to proceed with that as the input. --------------------------------------------- Talairach Tue Dec 21 18:22:57 EST 2004 /home/edamaraju/freesurfer/subjects/eFMRI02/mri talairach2 eFMRI02 INFO: registering eFMRI02 Tue Dec 21 18:22:57 EST 2004 -------------------------------------------- mri_convert orig orig/orig.mnc mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /home/edamaraju/freesurfer/subjects/eFMRI02/mri/transforms/talairach.xfm /home/edamaraju/freesurfer/subjects/eFMRI02/mri/orig /home/edamaraju/freesurfer/subjects/eFMRI02/mri/orig Tue Dec 21 18:24:00 EST 2004 --------------------------------------------- Nu Intensity Correction Tue Dec 21 18:24:00 EST 2004 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [edamaraju@brisbane.psych.brown.edu:/home/edamaraju/freesurfer/subjects/eFMRI02/mri/] [2004-12-21 18:24:09] running: /usr/pubsw04/packages04/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_13858/ nu/nu0.mnc nu/nu1.imp /usr/pubsw04/packages04/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++-libc6.1-1.so.2: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct -------------------------------------------------------------------------------- Where do I find these shared libraries? How should I link them? Any help is appreciated. Thanks, Eswar.

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tksurfer for MacOSX second try for those courageous people
by Yasunari Tosa 16 Dec '04

16 Dec '04

The issue was that MacOSX version of tksurfer could not read annotation file due to the bug in freesurfer code. My first try worked only at the developer desktops ;-) For those who are courageous, please try "again" the following "alpha" version. At least it worked at the original poster Brian at UCSD. (Thank you, Brian, for your patience.) There are three files provided at our ftp site: surfer.nmr.mgh.harvard.edu: use anonymous with your email address as a passwd. ftp> cd transfer/outgoing/birn/tosa/Mac ftp> bin ftp> get tix8.1.tar.gz ftp> get tksurfer ftp> get tksurfer.tcl IMPORTANT: 1. The tar file tix8.1.tar.gz must be extracted at /sw/lib so that you will end up having /sw/lib/tix8.1/* files. tksurfer will look for /sw/lib/tix8.1 directory for Tix initialization. (Another way is to read http://surfer.nmr.mgh.harvard.edu/faqomatic/cache/55.html (thanks to Kevin). install tix fink unstable package.) 2. Please keep the old tksurfer.tcl (rename it) just in case and replace it with the new one. This tksurfer uses Tcl/Tk 8.4 version, not 8.3. If you don't have these, don't install. Tosa Yasunari Tosa, Ph.D. Email: tosa(a)nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA

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mri_convert fix to address Analyze export
by Kevin Teich 16 Dec '04

16 Dec '04

We found a problem in writing Analyze format data. In particular, we were not writing the correct data_history orientation information, even though the .mat file was being written correctly. Since Freesurfer uses the .mat file if present, Freesurfer will not be affected by this bug. The problem is restricted to the case of using non-Freesurfer software to view or process Analyze data exported by Freesurfer. A new version of mri_convert fixes this bug. We're not releasing updates for the rest of the Freesurfer binaries that write data (and will write the incorrect Analyze volumes) in the interest of space, so if you are exporting Analyze data for use outside of Freesurfer, please use mri_convert as a final step. Thanks to Darren Weber and Graham Wideman for Analyze format information. Please see the README in the archive for more details. Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_convert-20041216-Linux.tar.gz Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_convert-20041216-Darwin.tar.gz -- Kevin Teich

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