Ongoing Problems: Bit of a delay having been away. Here is what I'm doing step by step and then the error message at the bottom. Again I am using CentOS5 Linux shell on a windows machine using Freesurfer V4.1.0 with the monitor settings on 32bit, and license file has been set up. Decided to try autorecon1 with the bert data:
*1) tcsh* *2) setenv FREESURFER_HOME home/user/Desktop/freesurfer* *3) setenv SUBJECTS home/user/Desktop/freesurfer/subjects * *4) 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 home/user/Desktop/freesurfer FSFAST_HOME home/user/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR home/user/Desktop/freesurfer/subjects MNI_DIR home/user/Desktop/freesurfer/mni * 5) source $FREESURFER_HOME/FreeSurferEnv.csh* -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME home/user/Desktop/freesurfer FSFAST_HOME home/user/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR home/user/Desktop/freesurfer/subjects MNI_DIR home/user/Desktop/freesurfer/mni *6) recon-all -s bert -autorecon1* INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.5-20081001 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 -rw-rw-rw- 1 user user 644862 Oct 4 09:08 /home/user/Desktop/freesurfer/subjects/bert/scripts/recon-all.log Linux localhost.localdomain 2.6.18-92.1.18.el5 #1 SMP Wed Nov 12 09:30:27 EST 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. mri_watershed: Command not found. mri_segment: Command not found. mri_label2label: Command not found. mri_em_register: Command not found. mri_ca_normalize: Command not found. mri_ca_register: Command not found. mri_ca_label: Command not found. mri_pretess: Command not found. mri_fill: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: 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. INFO: current FREESURFER_HOME does not match that of previous processing. Current: home/user/Desktop/freesurfer Previous: /usr/local/freesurfer/stable cp: cannot stat `home/user/Desktop/freesurfer/bin/recon-all': No such file or directory #-------------------------------------------- #...@# MotionCor Mon Dec 15 10:22:55 GMT 2008 Found 3 runs /home/user/Desktop/freesurfer/subjects/bert/mri/orig/001.mgz /home/user/Desktop/freesurfer/subjects/bert/mri/orig/002.mgz /home/user/Desktop/freesurfer/subjects/bert/mri/orig/003.mgz #----------------------------------------------- /home/user/Desktop/freesurfer/subjects/bert mri_motion_correct.fsl -o /home/user/Desktop/freesurfer/subjects/bert/mri/rawavg.mgz -wild /home/user/Desktop/freesurfer/subjects/bert/mri/orig/001.mgz /home/user/Desktop/freesurfer/subjects/bert/mri/orig/002.mgz /home/user/Desktop/freesurfer/subjects/bert/mri/orig/003.mgz mri_motion_correct.fsl: Command not found. Linux localhost.localdomain 2.6.18-92.1.18.el5 #1 SMP Wed Nov 12 09:30:27 EST 2008 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Mon Dec 15 10:22:55 GMT 2008 Many thanks for your help, - Chris On Wed, Nov 19, 2008 at 2:53 PM, Nick Schmansky <ni...@nmr.mgh.harvard.edu> wrote: > 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 >> <ni...@nmr.mgh.harvard.edu> 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 $FREESURFER_HOME/SetUpFreeSurfer.csh >> >> >> i noticed in your output it has the path as >> 'Desktop/freesurfer', which >> is not a full path, and probably that is why it is not finding >> the >> commands. >> >> Nick >> >> >> >> On Tue, 2008-11-18 at 16:04 +0000, Christian Lambert wrote: >> > I'm just starting out with freesurfer. I am using CentOS5 >> Linux shell >> > on a windows machine using Freesurfer V4.1.0 with the >> monitor settings >> > on 32bit. I have set up the license file and also configured >> > freesurfer as per the wiki pages: >> > >> > [u...@localhost ~]$ source >> $FREESURFER_HOME/SetUpFreeSurfer.csh >> > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 >> -------- >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > FREESURFER_HOME Desktop/freesurfer >> > FSFAST_HOME Desktop/freesurfer/fsfast >> > FSF_OUTPUT_FORMAT nii >> > SUBJECTS_DIR Desktop/freesurfer/subjects >> > MNI_DIR Desktop/freesurfer/mni >> > >> > >> > Now when I run recon all (using my own data) I get the >> following >> > error message: >> > >> > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub- >> v4.1.0 >> > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub- >> v4.1.0 >> > INFO: SUBJECTS_DIR is /home/user/Desktop/freesurfer/subjects >> > Actual FREESURFER_HOME /home/user/Desktop/freesurfer >> > Linux localhost.localdomain 2.6.18-92.1.13.el5 #1 SMP Wed >> Sep 24 >> > 19:33:52 EDT 2008 i686 athlon i386 GNU/Linux >> > mri_motion_correct.fsl: Command not found. >> > flirt: Command not found. >> > talairach_avi: Command not found. >> > tkregister2_cmdl: Command not found. >> > nu_correct: Command not found. >> > mri_normalize: Command not found. >> > .... >> > ... >> > .... >> > mris_make_surfaces: Command not found. >> > mris_register: Command not found. >> > mris_anatomical_stats: Command not found. >> > mrisp_paint: Command not found. >> > cp: cannot stat `Desktop/freesurfer/bin/recon-all': No such >> file or >> > directory >> > /home/user/Desktop/freesurfer/subjects/chris2 >> > >> > mri_watershed: Command not found. >> > >> > >> > I have been through the manual, wiki pages and seached the >> mailing >> > list extensively but could not find a solution to this >> problem. I >> > notice one similar thread in 2006 but it never detailed how >> the >> > problem was solved, but based on that I include the line >> below: >> > >> > [u...@localhost ~]$ 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 >> >> > >
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