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30078 discussions

recon-all exits with error
by Goradia, Dhruman D 01 Apr '08

01 Apr '08

Hello All, I have a library problem when I run recon-all. Recon-all exits with ERROR during the cortribbon step. I am using FC8 x86_64 OS on an Intel Xeon 64 bit machine. I have installed CentOS4-x86_64-v4.0.2 version of freesurfer. The library in question "libexpat.so.0" has been installed and is located in /usr/lib however, the problem persists. The command and error is: recon-all -s 24560 -cortribbon INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-r--r-- 1 giang users 698777 Apr 1 11:29 /usr/local/freesurfer/subjects/24560/scripts/recon-all.log Linux snood.wpic.upmc.edu 2.6.24.3-12.fc8 #1 SMP Tue Feb 26 14:21:30 EST 2008 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /Applications/freesurfer #-------------------------------------------- #@# Cortical ribbon mask Tue Apr 1 14:24:12 EDT 2008 /usr/local/freesurfer/subjects/24560/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 24560 mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory Linux snood.wpic.upmc.edu 2.6.24.3-12.fc8 #1 SMP Tue Feb 26 14:21:30 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Apr 1 14:24:12 EDT 2008 Any help is greatly appreciated. Thank you, Dhruman PS: Sorry if you received the email twice.

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qdec regression coeffs
by James N Porter 01 Apr '08

01 Apr '08

Hello All- When viewing the scalar overlays in qdec, how do I tell which coefficient is being displayed when I select "Regression Coefficients" from the menu? Having more than one regressor, I would expect more than one overlay of coefficients. Am I missing something very elementary? -- --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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structures list
by Lindsay Casmaer 01 Apr '08

01 Apr '08

Does the website contain a list of structures labeled in both version 3 and version 4? I am looking for both cortical and subcortical segmentation labels. Thanks, Lindsay

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recon-all exits with errors
by Goradia, Dhruman D 01 Apr '08

01 Apr '08

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glm_fit question...
by Cameron Ellis 01 Apr '08

01 Apr '08

Hi all, Is it necessary to include a value in your contrast matrix for every class and variable in your fsgd file? It seems that this is the case. My understanding is that if you weight a variable 0 then it is automatically controlled for. So if am required to weight a variabe in the contrast matrix that do not want to control for, then to not control for it I have to make a different fsgd file without that variable? Thanks, Cameron

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unable to load flat.asc in MATLAB
by SHRIKANTH KULASHEKHAR 01 Apr '08

01 Apr '08

Hi, I have been trying to plot flattened cortex surfaces using MATLAB but have been unsuccessful so far. After flattening the cortex in freesurfer, I convert in into an ascii file by using: mris_convert -p label1.flat label1.flat.asc But then fail to read the *.asc file as a patch in MATLAB using the read_asc.m from the Freesurfer MATLAB toolbox. Are there any other MATLAB codes to read and plot the *.flat.asc files ? Thank you. Shriks Share files, take polls, and discuss your passions - all under one roof. Go to http://in.promos.yahoo.com/groups

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Cannot download new Leopard release
by Juergen Haenggi 01 Apr '08

01 Apr '08

Dear FS experts I tried to download freesurfer-Darwin-tiger-i686-stable-pub-v4.0.3-full.dmg but when I klicked on the link on your website the following error occurred. 550: Failed to change directory This did not occurred when I downloaded the CENTOS release Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Fwd: segmentation fault error, mri_ca_register
by Teddy Youn 31 Mar '08

31 Mar '08

i incompletely copied the error message from recon-all.log: gca peak Unknown = 0.94091 ( 0) gca peak Left_Inf_Lat_Vent = 0.14709 (39) gca peak CSF = 0.14344 (47) gca peak Left_Accumbens_area = 0.20088 (67) gca peak Left_undetermined = 0.98433 (34) gca peak Left_vessel = 0.32698 (60) gca peak Left_choroid_plexus = 0.11007 (56) gca peak Right_Inf_Lat_Vent = 0.20176 (34) gca peak Right_Accumbens_area = 0.32293 (69) gca peak Right_vessel = 0.36466 (58) gca peak Right_choroid_plexus = 0.09865 (51) gca peak Fifth_Ventricle = 0.66382 (40) gca peak WM_hypointensities = 0.12408 (82) gca peak non_WM_hypointensities = 0.07897 (54) gca peak Optic_Chiasm = 0.38389 (74) Segmentation fault ERROR: mri_ca_register with non-zero status Darwin swmed-xryrdix93 9.2.0 Darwin Kernel Version 9.2.0: Tue Feb 5 16:13:22 PST 2008; root:xnu-1228.3.13~1/RELEASE_I386 i386 i386 recon-all exited with ERRORS at Mon Mar 31 00:16:42 CDT 2008 Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

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segmentation fault error, mri_ca_register
by Teddy Youn 31 Mar '08

31 Mar '08

Hi all, I have a scan of a patient that I've tried troubleshooting via the listserv and fswiki, but with no success. Generally, during mri_ca_register, I end up with a segmentation fault of the following: ----------------- gca peak Unknown = 0.94091 ( 0) gca peak Left_Inf_Lat_Vent = 0.14709 (39) gca peak CSF = 0.14344 (47) gca peak Left_Accumbens_area = 0.20088 (67) gca peak Left_undetermined = 0.98433 (34) gca peak Left_vessel = 0.32698 (60) gca peak Left_choroid_plexus = 0.11007 (56) gca peak Right_Inf_Lat_Vent = 0.20176 (34) gca peak Right_Accumbens_area = 0.32293 (69) gca peak Right_vessel = 0.36466 (58) gca peak Right_choroid_plexus = 0.09865 (51) gca peak Fifth_Ventricle = 0.66382 (40) gca peak WM_hypointensities = 0.12408 (82) gca peak non_WM_hypointensities = 0.07897 (54) gca peak Optic_Chiasm = 0.38389 (74) Segmentation fault [swmed-xryrdix93:CorrectedBrainsGE/TBI/St43] teresa% --------- I can forward a recon-all.log of this subject. I've also had some major issues with intensity inhomogeneities where the pial, wm, and orig surfaces will not pick up the sulci in certain regions of the cortex (the wm -aux volume just looks like one big blob of grey). I've tried using -nuiterations 4, 150, etc., but have not had much success. Any suggestions would be greatly appreciated. Warm Regards, -t Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

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error while loading shared libraries:libtiff.so.3
by Lúcia Garrido 30 Mar '08

30 Mar '08

Hello, I'm using Debian and downloaded freesurfer-Linux-centos4-stable-pub-v4.0.2-full.tar.gz. Everything worked fine when I tested the installation with tkmedit and tksurfer. I then ran recon-all -i C04_SS.nii -autorecon1 -s C04_SS and it also finished without errors. But when I ran recon-all -autorecon2 -s C04_SS, there was an error at the end saying: mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory I've checked the shared libraries and I have libtiff.so.4. Could you let me know how to get libtiff.so.3 to work and if I should do something else? Thank you very much. Lucia

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