try the command: sudo apt-get install tcl
-- PPJ Please: cc the freesurfer list when answering 2011/2/22 Carolina Valencia <cvalen...@linkdx.com.co> > Hi Pedro, > > Finally, I could install it with the license file and the environment is > properly set without warnings. > But trying to test it, following the instruction on the wiki page I have a > problem > > cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz > /usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio. > > in the .bashrc I copy the right location of the freesurfer folder > FREESURFER_HOME=/home/cvalencia/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > > 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <p...@netfilter.com.br> > >> run this command >> >> sudo rm -rf $FREESURFER_HOME >> >> >> >> 2011/2/21 Carolina Valencia <cvalen...@linkdx.com.co> >> >>> Thanks Pedro, >>> >>> How I uninstall that version to re-install the correct version? >>> I look for some answers and try >>> >>> rm -rf $FREESURFER_HOME >>> >>> It says that I don't have permission,how I can unistall it, if i'm the >>> admin user? >>> >>> Thanks in advance, >>> >>> Carolina >>> >>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <p...@netfilter.com.br >>> > >>> >>>> It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS >>>> >>>> >>>> 2011/2/21 Carolina Valencia <cvalen...@linkdx.com.co> >>>> >>>> >>>>> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae >>>>> #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < >>>>> p...@netfilter.com.br> >>>>> >>>>> Please send the result of the command: >>>>>> >>>>>> uname -a >>>>>> >>>>>> >>>>>> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < >>>>>> cvalen...@linkdx.com.co> wrote: >>>>>> >>>>>>> Hi Bruce, >>>>>>> >>>>>>> I'm experimenting problems with the installation on Ubuntu too. >>>>>>> There's is warning in the welcome message, it seems that something is >>>>>>> missing: >>>>>>> >>>>>>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- >>>>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>>>>> WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist >>>>>>> FREESURFER_HOME /home/cvalencia/Descargas/freesurfer >>>>>>> FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast >>>>>>> FSF_OUTPUT_FORMAT nii >>>>>>> SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects >>>>>>> MNI_DIR /home/cvalencia/Descargas/freesurfer/mni >>>>>>> FSL_DIR /usr/share/fsl/4.1 >>>>>>> >>>>>>> >>>>>>> I try to test it and it shows >>>>>>> cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit >>>>>>> /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de >>>>>>> ejecutable incorrecto. Binary file not executable. >>>>>>> >>>>>>> Thanks a lot, >>>>>>> >>>>>>> Carolina >>>>>>> >>>>>>> 2011/2/18 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>>>>> >>>>>>>> Hi Jie, >>>>>>>> >>>>>>>> what hardware are you using? Is it a 64 bit operating system? >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> >>>>>>>> On Sat, 19 Feb 2011, Liukarl wrote: >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Hello, Freesurfer experts: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I am new to freesurfer and try to >>>>>>>>> install the newest version of freesurfer in Ubuntu system. I >>>>>>>>> closely >>>>>>>>> followed the instructions, and the only difference is that I >>>>>>>>> installed it in my Documents, instead of local folder. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Below is the output after “source >>>>>>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh” >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -------- >>>>>>>>> freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- >>>>>>>>> >>>>>>>>> Setting up environment for >>>>>>>>> FreeSurfer/FS-FAST (and FSL) >>>>>>>>> >>>>>>>>> FREESURFER_HOME >>>>>>>>> /home/jie/Documents/freesurfer/ >>>>>>>>> >>>>>>>>> FSFAST_HOME >>>>>>>>> /home/jie/Documents/freesurfer//fsfast >>>>>>>>> >>>>>>>>> FSF_OUTPUT_FORMAT nii >>>>>>>>> >>>>>>>>> SUBJECTS_DIR >>>>>>>>> /home/jie/Documents/freesurfer//subjects >>>>>>>>> >>>>>>>>> MNI_DIR >>>>>>>>> /home/jie/Documents/freesurfer//mni >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Everything seems fine and I also added >>>>>>>>> the .license file to the freesurfer folder. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> But when I test it by “tkmedit bert >>>>>>>>> orig.mgz”, it reponds “Illegal instruction” >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> If I type in “recon-all”, it will >>>>>>>>> show >>>>>>>>> >>>>>>>>> “ Required Arguments: >>>>>>>>> >>>>>>>>> -subjid <subjid> >>>>>>>>> >>>>>>>>> -<process directive>…... >>>>>>>>> ” >>>>>>>>> and the other arguments. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> How to fix the problem and make >>>>>>>>> Fressurfer run? Any help is appreciated. Thanks a lot! >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Jie >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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. >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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. >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >>> -- >>> >> >> > > > -- >
_______________________________________________ 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.
