Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30061 discussions

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

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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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Fw: csurf failure
by Tetsuya Iidaka 09 Dec '04

09 Dec '04

Dear experts. I installed FreeSurfer (Snapshot full version) on Linux(recent version of TurboLinux) Pentium4 PC. Source SetUpFreeSurfer.csh process was successful, but when I entered "csurf" command, following error message appeared. "/home/XXX/freesurfer//bin/noarch/csurf: permission denied" .license file is in /freesurfer/ directory. Any help is very much appreciated. Tetsuya Iidaka Dept of Psychology, Nagoya University iidaka(a)info.human.nagoya-u.ac.jp

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how to set the number of vertex ?
by tulu 09 Dec '04

09 Dec '04

Dear freesurfer expert, I am a new user of freesurfer. When I use mri_tessellate, how to set the number of vertex ? Thanks replay JLH

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mris_anatomical_stats
by Calabrese Massimiliano 08 Dec '04

08 Dec '04

Hi everybody, Currently, we can use mris_anatomical_stats to report statistics such as thickness +/- std. dev. over the list of brain regions, as created by the parcellate_subject program. We are wondering if it is currently possible to produce similar statistics, but not just on thickness, etc., but also on data that we can supply externally. For example, we can create a file that contains a list of nodes and corresponding data values. Is it possible to have the mris_anatomical_stats program create statistics on a region-by-region basis from our supplied data? Thanks a lot for your help Massimiliano Calabrese Imaging Group NeuroImmunology Branch NIDS, NIH and Rick Reynolds SSCC/NIMH/NIH

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Stats and viewing parcellation problem
by Brian Schweinsburg, Ph.D. 07 Dec '04

07 Dec '04

Hi All, I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints? In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem? My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218. I appreciate any assistance. Brian ####### mris_anatomical_stats error message ####### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error ####### Tksurfer error message ####### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory Command Finished

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