Andrew,

When the freesurfer script is run, that is, when you type:

source $FREESURFER_HOME/SetUpFreeSurfer.csh

does it output any error messages? You should see something like:

-------- freesurfer-Linux-centos4-stable-v3.0.5-20070717 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable FSFAST_HOME /usr/local/freesurfer/stable/fsfast SUBJECTS_DIR /autofs/space/minerva_001/users/nicks/subjects MNI_DIR /usr/local/freesurfer/stable/mni GSL_DIR /usr/local/freesurfer/stable/lib/gsl FSL_DIR /usr/local/freesurfer/stable/fsl

Which Linux OS are you using and which freesurfer distribution was installed?

Nick

On Tue, 2007-07-24 at 12:16 -0400, Andrew Ellison wrote:

Hey all

so when i run recon-all after ive set up all my subjects directories (previous issue) i am told the following

[root@ebrcb-dhcp-240-47 freesurfer]# recon-all -autorecon1 -subjid 060615_26SS INFO: SUBJECTS_DIR is /usr/subjects/athpro/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 7014 Jul 24 11:58 /usr/subjects/athpro/freesurfer/060615_26SS/scripts/recon- all.log Linux ebrcb-dhcp-240-47.bumc.bu.edu 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory strings: 'mritotal:': No such file strings: 'Command': No such file strings: 'not': No such file strings: 'found.': No such file nu_correct: Command not found. mri_normalize: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_watershed: error while loading shared libraries: libgsl.so.0 : cannot open shared object file: No such file or directory mri_segment: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_fill: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_tessellate: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_smooth: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_inflate: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_sphere: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_fix_topology: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_euler_number: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_make_surfaces: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mrisp_paint: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_label2label: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_em_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_normalize: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_label: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory #-------------------------------------------- #@# MotionCor Tue Jul 24 12:06:18 EDT 2007 ERROR: no run data found in /usr/subjects/athpro/freesurfer/060615_26SS/mri. Make sure to have a volume called 001.mgz in /usr/subjects/athpro/freesurfer/060615_26SS/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux ebrcb-dhcp-240-47.bumc.bu.edu 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux

recon-all exited with ERRORS at Tue Jul 24 12:06:18 EDT 2007

although the gsl is in its proper place and when i manually setenv it still claims cannot open shared object and what not, any help? thanks

Andy

i think im posting this, apologies if im not _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer