After doing an upgrade from fedora 17 to fedora 18,I am trying to execute the installation tests, I can't start "$tkmedit", tksurfer or mri_convert. But freeview and qdec seem to be good. Tested with a CentOS4 or a CentOS6 recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $ -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl --------- Linux version 3.8.5-201.fc18.x86_64 (mockbuild@bkernel02) (gcc version 4.7.2 20121109 (Red Hat 4.7.2-8)) processor:Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz tcsh 6.18.00 (Astron) 2012-01-14 -------------------- When I do: tkmedit bert orig.mgz, it returned, ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : ----------------------- When I do: tksurfer bert rh pial, it returned, subject is bert hemi is rh surface is pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/fallsi/Protocoles checking for nofix files in 'pial' Reading image info (/usr/local/freesurfer/subjects/bert) Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/orig.mgz
------------------- When I start mri_convert, I have this error message: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from IM1... Segmentation fault (core dumped) --------------- the contents of .xdebug_tkmedit: tkmedit started: Wed Apr 3 11:43:32 2013
/usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz
$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /home/fallsi/Protocoles Set subject home dir to /usr/local/freesurfer/subjects/bert
Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27675600, isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=/usr/local/freesurfer/tktools/tkmedit.bin ) 02: Loading volume orig.mgz 01: main() 01: Parsing command line arguments 00: 00: ---------------------- Thank you in advance,
Did you try running the freesurfer CentOS6 version on the upgraded version of Fedora?
-Zeke
On 04/03/2013 08:09 AM, Sidy Fall wrote:
After doing an upgrade from fedora 17 to fedora 18,I am trying to execute the installation tests, I can't start "$tkmedit", tksurfer or mri_convert. But freeview and qdec seem to be good. Tested with a CentOS4 or a CentOS6 recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $ -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl
Linux version 3.8.5-201.fc18.x86_64 (mockbuild@bkernel02) (gcc version 4.7.2 20121109 (Red Hat 4.7.2-8)) processor:Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz tcsh 6.18.00 (Astron) 2012-01-14
When I do: tkmedit bert orig.mgz, it returned, ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu : : Now exiting... :
When I do: tksurfer bert rh pial, it returned, subject is bert hemi is rh surface is pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/fallsi/Protocoles checking for nofix files in 'pial' Reading image info (/usr/local/freesurfer/subjects/bert) Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/orig.mgz
When I start mri_convert, I have this error message: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from IM1... Segmentation fault (core dumped)
the contents of .xdebug_tkmedit: tkmedit started: Wed Apr 3 11:43:32 2013
/usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /home/fallsi/Protocoles Set subject home dir to /usr/local/freesurfer/subjects/bert
Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27675600, isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=/usr/local/freesurfer/tktools/tkmedit.bin ) 02: Loading volume orig.mgz 01: main() 01: Parsing command line arguments 00: 00:
Thank you in advance,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I can confirm the problem with Fedora 18 is that former glibc version would accept unsupported salt values, but newer versions of the library have become stricter. More details at https://bugzilla.redhat.com/show_bug.cgi?id=905638
I can also say you can run tkmedit, tksurfer and freeview if you install virtualbox and create a Virtual Machine with CentOS6 64 bit. However I have problems with recon-all tests. Posted the following before and waiting for any help
Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over Fedora 18 using VirtualBox 4.2.8. Tkmedit, Tksurfer, qdec and freeview all work great. But recon-all tests return errors. Thanks in advance for your help.
_______________________________________ recon-all -s bert -autorecon1 running loop to estimate saturation parameter: A or b constain NAN or infinity values!! _______________________________________ recon-all -s bert -all talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
_______________________________________ The log indicated above shows: imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted
2013/4/3 zkaufman@nmr.mgh.harvard.edu zkaufman@nmr.mgh.harvard.edu
Did you try running the freesurfer CentOS6 version on the upgraded version of Fedora?
-Zeke
On 04/03/2013 08:09 AM, Sidy Fall wrote:
After doing an upgrade from fedora 17 to fedora 18,I am trying to execute the installation tests, I can't start "$tkmedit", tksurfer or mri_convert. But freeview and qdec seem to be good. Tested with a CentOS4 or a CentOS6 recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $ -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl
Linux version 3.8.5-201.fc18.x86_64 (mockbuild@bkernel02) (gcc version 4.7.2 20121109 (Red Hat 4.7.2-8)) processor:Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz tcsh 6.18.00 (Astron) 2012-01-14
When I do: tkmedit bert orig.mgz, it returned, ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu : : Now exiting... :
When I do: tksurfer bert rh pial, it returned, subject is bert hemi is rh surface is pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/fallsi/Protocoles checking for nofix files in 'pial' Reading image info (/usr/local/freesurfer/subjects/bert) Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/orig.mgz
When I start mri_convert, I have this error message: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from IM1... Segmentation fault (core dumped)
the contents of .xdebug_tkmedit: tkmedit started: Wed Apr 3 11:43:32 2013
/usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /home/fallsi/Protocoles Set subject home dir to /usr/local/freesurfer/subjects/bert
Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27675600, isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=/usr/local/freesurfer/tktools/tkmedit.bin ) 02: Loading volume orig.mgz 01: main() 01: Parsing command line arguments 00: 00:
Thank you in advance,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
-
Marcos Martins da Silva -
Sidy Fall -
zkaufman＠nmr.mgh.harvard.edu