Christian, You may want to try explicitly setting your freesurfer home prior to sourcing, like this:
setenv FREESURFER_HOME /home/user/Desktop/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh i noticed in your output it has the path as 'Desktop/freesurfer', which is not a full path, and probably that is why it is not finding the commands. Nick On Tue, 2008-11-18 at 16:04 +0000, Christian Lambert wrote: > I'm just starting out with freesurfer. I am using CentOS5 Linux shell > on a windows machine using Freesurfer V4.1.0 with the monitor settings > on 32bit. I have set up the license file and also configured > freesurfer as per the wiki pages: > > [EMAIL PROTECTED] ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.csh > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME Desktop/freesurfer > FSFAST_HOME Desktop/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR Desktop/freesurfer/subjects > MNI_DIR Desktop/freesurfer/mni > > > Now when I run recon all (using my own data) I get the following > error message: > > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 > INFO: SUBJECTS_DIR is /home/user/Desktop/freesurfer/subjects > Actual FREESURFER_HOME /home/user/Desktop/freesurfer > Linux localhost.localdomain 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 > 19:33:52 EDT 2008 i686 athlon i386 GNU/Linux > mri_motion_correct.fsl: Command not found. > flirt: Command not found. > talairach_avi: Command not found. > tkregister2_cmdl: Command not found. > nu_correct: Command not found. > mri_normalize: Command not found. > .... > ... > .... > mris_make_surfaces: Command not found. > mris_register: Command not found. > mris_anatomical_stats: Command not found. > mrisp_paint: Command not found. > cp: cannot stat `Desktop/freesurfer/bin/recon-all': No such file or > directory > /home/user/Desktop/freesurfer/subjects/chris2 > > mri_watershed: Command not found. > > > I have been through the manual, wiki pages and seached the mailing > list extensively but could not find a solution to this problem. I > notice one similar thread in 2006 but it never detailed how the > problem was solved, but based on that I include the line below: > > [EMAIL PROTECTED] ~]$ ldd 'which mri_convert' > ldd: ./which mri_convert: No such file or directory > > Thanks for any insight you can provide. > > _______________________________________________ > 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
