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.
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