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