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
<ni...@nmr.mgh.harvard.edu <mailto: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 <mailto: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
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
>
------------------------------------------------------------------------
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--
Christian Scheel
Thielenstraße 15
50825 Köln
Tel: 0221-9983001
Mobil: 01515-9268691
Skype: demibee
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