Hi Z K, Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one installed with the latest freesurfer version did not work while others finished the processing in a reasonable processing time and I got the results.
Also, I have a PC at my office installed with the latest freesurfer version and it works fine. So I have two PCs installed with the latest Freesurfer (one of them which does not work is in the lab). To summarize: All PCs (16 PCs in the lab and 1 in my office) are installed with latest Ubuntu version 14.04 64 bits 15 PCs in the lab are installed with freesurfer 5.0.0 version 1 PC in the lab is installed with the latest freesurfer version (does not work, permission denied) 1 PC in my office is installed with the latest freesurfer version (works fine) All these PCs have Ubuntu 14.04 64bit installed on them. No, I am not using any vitual machine. Regarding the root user, I will try it on Sunday as I am away for a couple of days. Many thanks for your continuous support. Ali On Thu, Oct 30, 2014 at 6:34 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > Ali, > > First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are > working properly? I am under the impression that versions of freesurfer > pre-version 5.3 will not work on newer linux distributions? > > > In regards to your current permision denied issue... What happens if you > try and run tkmedit as root user? Also, you not using virtual machine > setup are you? > > -Zeke > > On 10/30/2014 06:27 AM, Ali Radaideh wrote: > > It does not work. This is really strange > > > > On Thu, Oct 30, 2014 at 12:53 AM, Z K <zkauf...@nmr.mgh.harvard.edu > > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: > > > > I beleive it should have a lower case X, as in: > > > > chmod -R a+x freesurfer/bin > > > > -Zeke > > > > On 10/28/2014 01:19 AM, Ali Radaideh wrote: > > > Dear Douglas > > > > > > Thanks for your reply. unfortunatey I still get the same error. > > Here is > > > the terminal output. Is there anything else I can do? > > > > > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > -------- > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > FREESURFER_HOME /usr/local/freesurfer > > > FSFAST_HOME /usr/local/freesurfer/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > > MNI_DIR /usr/local/freesurfer/mni > > > FSL_DIR /usr/local/fsl > > > imaging@imaging-ThinkCentre-23:~$ tcsh > > > imaging-ThinkCentre-23:~> tkmedit > > > /usr/local/freesurfer/bin/tkmedit: Permission denied. > > > imaging-ThinkCentre-23:~> > > > > > > > > > On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > > > > Try chmod -R a+X freesurfer/bin > > > > > > > > > On 10/26/14 1:57 PM, Ali Radaideh wrote: > > >> Dear FreeSurfer users, > > >> > > >> I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One > > of the > > >> PCs has the latest version of freesurfer 5.3.0 while the > others > > >> have the version 5.0.0. The PC that is installed with the > latest > > >> version freesurfer 5.3.0 does not allow me to run any > > command and > > >> everytime I try a command such such as tkmedit i get the > > following > > >> error > > >> /usr/local/freesurfer/bin/tkmedit: permission denied. > > >> > > >> I have tried to change the permission settings > > >> sudo chown -R imaging:imaging freesurfer > > >> > > >> but did not work. > > >> > > >> Any ideas why is this happening although I have done the same > > >> thing to other PCs and they are working fine. > > >> > > >> Thanks in advance, > > >> Ali > > >> > > >> -- > > >> /Ali M. Al-Radaideh. PhD > > >> Assistant Professor > > >> Head of Department of Medical Imaging > > >> Vice Dean of the Faculty of Allied Health Sciences > > >> The Hashemite University, > > >> Zarqa, Jordan > > >> W.phone +962 5 3903333 ext.5422, 5355, 5364 > > >> Email: ali.radai...@hu.edu.jo > > <mailto:ali.radai...@hu.edu.jo> <mailto:ali.radai...@hu.edu.jo > > <mailto:ali.radai...@hu.edu.jo>> > > >> / > > >> /webpage: > http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > >> > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto: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. If you believe this e-mail was sent to you in > > error and > > > the e-mail > > > contains patient information, please contact the Partners > > Compliance > > > HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent > to > > > you in error > > > but does not contain patient information, please contact the > > sender > > > and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > -- > > > /Ali M. Al-Radaideh. PhD > > > Assistant Professor > > > Head of Department of Medical Imaging > > > Vice Dean of the Faculty of Allied Health Sciences > > > The Hashemite University, > > > Zarqa, Jordan > > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > > Email: ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo> > > <mailto:ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>> > > > / > > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > /Ali M. Al-Radaideh. PhD > > Assistant Professor > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo> > > / > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
_______________________________________________ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
