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 nicks@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:
    >
    > [user@localhost ~]$ source
    $FREESURFER_HOME/SetUpFreeSurfer.csh
    > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0
    --------
    > Setting up environment for FreeSurfer/FS-FAST (and FSL)
    > FREESURFER_HOME   Desktop/freesurfer
    > FSFAST_HOME       Desktop/freesurfer/fsfast
    > FSF_OUTPUT_FORMAT nii
    > SUBJECTS_DIR      Desktop/freesurfer/subjects
    > MNI_DIR           Desktop/freesurfer/mni
    >
    >
    > Now when I  run recon all (using my own data) I get the
    following
    > error message:
    >
    > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-
    v4.1.0
    > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-
    v4.1.0
    > INFO: SUBJECTS_DIR is /home/user/Desktop/freesurfer/subjects
    > Actual FREESURFER_HOME /home/user/Desktop/freesurfer
    > Linux localhost.localdomain 2.6.18-92.1.13.el5 #1 SMP Wed
    Sep 24
    > 19:33:52 EDT 2008 i686 athlon i386 GNU/Linux
    > mri_motion_correct.fsl: Command not found.
    > flirt: Command not found.
    > talairach_avi: Command not found.
    > tkregister2_cmdl: Command not found.
    > nu_correct: Command not found.
    > mri_normalize: Command not found.
    > ....
    > ...
    > ....
    > mris_make_surfaces: Command not found.
    > mris_register: Command not found.
    > mris_anatomical_stats: Command not found.
    > mrisp_paint: Command not found.
    > cp: cannot stat `Desktop/freesurfer/bin/recon-all': No such
    file or
    > directory
    > /home/user/Desktop/freesurfer/subjects/chris2
    >
    > mri_watershed: Command not found.
    >
    >
    > I have been through the manual, wiki pages and seached the
    mailing
    > list extensively but could not find a solution to this
    problem. I
    > notice one similar thread in 2006 but it never detailed how
    the
    > problem was solved, but based on that I include the line
    below:
    >
    > [user@localhost ~]$ 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

Christian,

I think the paths are still not correct. Try using

/home/user/Desktop....

instead of

home/user/Desktop...

Also in 3) the variable of the subject directory is called SUBJECTS_DIR instead of SUBJECTS so the command should be: setenv SUBJECTS_DIR /home/user/Desktop/freesurfer/subjects

Best wishes, Christian Scheel

--- University of Cologne Department of Psychiatry

Christian Lambert schrieb:

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 <nicks@nmr.mgh.harvard.edu mailto:nicks@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 <nicks@nmr.mgh.harvard.edu mailto:nicks@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:
    >
    > [user@localhost ~]$ source
    $FREESURFER_HOME/SetUpFreeSurfer.csh
    > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0
    --------
    > Setting up environment for FreeSurfer/FS-FAST (and FSL)
    > FREESURFER_HOME   Desktop/freesurfer
    > FSFAST_HOME       Desktop/freesurfer/fsfast
    > FSF_OUTPUT_FORMAT nii
    > SUBJECTS_DIR      Desktop/freesurfer/subjects
    > MNI_DIR           Desktop/freesurfer/mni
    >
    >
    > Now when I  run recon all (using my own data) I get the
    following
    > error message:
    >
    > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-
    v4.1.0
    > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-
    v4.1.0
    > INFO: SUBJECTS_DIR is /home/user/Desktop/freesurfer/subjects
    > Actual FREESURFER_HOME /home/user/Desktop/freesurfer
    > Linux localhost.localdomain 2.6.18-92.1.13.el5 #1 SMP Wed
    Sep 24
    > 19:33:52 EDT 2008 i686 athlon i386 GNU/Linux
    > mri_motion_correct.fsl: Command not found.
    > flirt: Command not found.
    > talairach_avi: Command not found.
    > tkregister2_cmdl: Command not found.
    > nu_correct: Command not found.
    > mri_normalize: Command not found.
    > ....
    > ...
    > ....
    > mris_make_surfaces: Command not found.
    > mris_register: Command not found.
    > mris_anatomical_stats: Command not found.
    > mrisp_paint: Command not found.
    > cp: cannot stat `Desktop/freesurfer/bin/recon-all': No such
    file or
    > directory
    > /home/user/Desktop/freesurfer/subjects/chris2
    >
    > mri_watershed: Command not found.
    >
    >
    > I have been through the manual, wiki pages and seached the
    mailing
    > list extensively but could not find a solution to this
    problem. I
    > notice one similar thread in 2006 but it never detailed how
    the
    > problem was solved, but based on that I include the line
    below:
    >
    > [user@localhost ~]$ 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 

mailto:Freesurfer@nmr.mgh.harvard.edu

...

...

    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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