Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

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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skull strip
by Tetsuya Iidaka 14 Dec '04

14 Dec '04

Dear experts, Thank you for answering basic question. Iam using Linux version of Freesurfer on Pen4 PC, and trying to run "Process Volume" with my anatomical data which was acquired by Siemens Allegra 3T maschine and converted to analyze format. "conversion" and "normalize intensities" were OK and COR001-COR256 were written in "orig" and "T1" directory. but next process failed and following message appeared. No COR-XXX file is written in "brain" directory. New mri-watershed" file is in bin/Linux directory as indicated by mailing list. Thanks in advance Tetsuya Iidaka Nagoya University Department of Psychology iidaka(a)info.human.nagoya-u.ac.jp ------------------------------------------------------------- /home/XXX/freesurfer//bin/Linux/mri_watershed /home/XXX/freesurfer/subjects/test01/mri/T1 /home/XXX/freesurfer/subjects/test01/mri/brain ************************************************************ The input file is /home/XXX/freesurfer/subjects/test01/mri/T1 The output file is /home/XXX/freesurfer/subjects/test01/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Find the largest 110-component... Command Finished -----------------------------------------------------------------

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white matter fill
by Kai Schreiber 13 Dec '04

13 Dec '04

Hi, -what might be causing freesurfer to go through the motions of doing the white matter fill without actually writing any files? I do not find an error message anywhere, the status window shows the fill as "done", but processing stops, because there are no files created. Cheers, Kai

2 1

pial surface ill defined
by Kai Schreiber 10 Dec '04

10 Dec '04

Hi, when we fit a surface to our anatomical data, everything works fine without error messages. However, looking at the fitted surfaces in the end, the original surface / white matter boundary looks fairly good, while the pial surface is not at all related to gray matter and follows the original surface very poorly. Also, it quite frequently runs across the original surface. Are we doing anything wrong? Kai

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