After you run the 'source $FREESURFER_HOME/SetUpFreeSurfer.csh' command, is /home/user/Desktop/freesurfer in your 'path' environment variable?
On Wed, 2008-11-19 at 11:25 +0000, Christian Lambert wrote: > I have explicitly set it like Nick suggested and ensured I have also > sourced FreeSurferEnv.csh. Same result unfortunately. > > On Tue, Nov 18, 2008 at 5:08 PM, Nick Schmansky > <[EMAIL PROTECTED]> wrote: > 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
