Hi Efrat - This appears to be a virtual machine problem:
https://communities.vmware.com/thread/312591?tstart=0
There are some solutions suggested in that thread. I'm wondering if using
a relative instead of an absolute path for the symlink works, i.e.,
ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
instead of:
ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
Can you please try it both ways and let me know if the former works on a
computer where the latter doesn't?
And yes, if you fix error #1 it'll fix error #2 as well.
Thanks,
a.y
On Tue, 29 Mar 2016, Efrat Kliper wrote:
Dear Freesurfer experts,
I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has
already been completed in Freesurfer 5.1) in order to run some new functions
of Tracula (I have also installed the latest Tracula update
(tracula.update.centos4_x86_64.5.3.2014_05_26).
I am using:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
RedHat release: CentOS release 5.3 (Final)
Kernel info: Linux 2.6.18-128.1.6.el5 x86_64
I encountered two problems:
1. When I run the initial code of Tracula: trac-all –prep code:
/home/fsl/
usr/local/freesurfer/bin/trac-all -prep -c
/mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt
Subject TB_480
SUBJECTS_DIR /mnt/hgfs/linux_share/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
fsl
localhost.localdomain
Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT
2009 x86_64 x86_64 x86_64 GNU/Linux
I am getting the following message: ln -sf
/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
ln: creating symbolic link
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not
supported
2. If I run the trac-all –bedp command of Tracula (on already trac-all
data which was preproc on Freesurfer version 5.1. /home/fsl
/usr/local/freesurfer/bin/trac-all
-bedp -c /home/fsl/Desktop/xxx.txt
Subject TB_201
SUBJECTS_DIR /mnt/hgfs/linux_share/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
fsl
localhost.localdomain
Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT
2009 x86_64 x86_64 x86_64 GNU/Linux
I am getting the following message:
Program versions:
$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name:
$ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Aug 16 2014 05:13:24
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: fsl
Machine: localhost.localdomain Platform: Linux PlatformVersion:
2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400
FLIRT version 6.0
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name:
$ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06
CVS: User: fsl Machine: localhost.localdomain Platform: Linux
PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name:
$ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35
CVS: User: fsl Machine: localhost.localdomain Platform: Linux
PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name:
$ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35
CVS: User: fsl Machine: localhost.localdomain Platform: Linux
PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion:
$Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013
22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux
PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion:
$Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014
05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux
PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name:
$ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35
CVS: User: fsl Machine: localhost.localdomain Platform: Linux
PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /mnt/hgfs/linux_share/subjects/TB_201/dmri
subjectdir is /mnt/hgfs/linux_share/subjects/TB_201/dmri
/mnt/hgfs/linux_share/subjects/TB_201/dmri/data not found
I am guessing those problems are from the same source.
Do you have any suggestions on how can I resolve these issues?
Is there a way to overcome the "ln" command and to create this data file
without it?
(I have also tried to run it from local OS linux and not from shared folder.
Many thanks,
Efrat
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