Dear Anastasia,
Thank you for the fast replay. I have tried both suggestions, however it still reports: Operation not supported Also, I have used the links that you have sent me but non work. This time (after changing according to the links), I got the message: operation denied I don’t know how to resolve the issue of virtual machine, as not much is written about that and the links are not helping with that issue. Do you have other suggestions regarding how to change the script, so it will create the data.nii without the symbolic link (there are plenty "ln" commands uses in the script)? Many thanks, Efrat On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > 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 >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. 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