Hi I’ve previously encountered the same error. I’ve also tried to change permission but that didn’t really work out for me. I have fixed it by installing libjpeg62-dev: Maybe the following command could fix your problem too?
sudo apt-get install libjpeg62-dev Hope this might work for you? Cheers Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be > On 31 Oct 2014, at 16:35, zkauf...@nmr.mgh.harvard.edu wrote: > > Yes, please try running as root and get back when you have the chance. > This is a very odd issue and your results when running as root will > provide insight. > > -Zeke > >> 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. >>>>>> >>>>>> âThanks in advance, >>>>>> Aliâ >>>>>> >>>>>> -- >>>>>> /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>> >>>> <mailto: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=/ >>> <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>> >>>> <mailto: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 >>>>>> <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>> >>>> <mailto: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>> >>>> <mailto: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=/ >>>>> <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 >>>>> <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 >>>> <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> >>>> <mailto:ali.radai...@hu.edu.jo <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <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 >>> <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 <mailto:ali.radai...@hu.edu.jo> >> <ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>>* >> *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= >> <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=> >> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 > <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 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.
