try the command:
sudo apt-get install tcl
-- PPJ
Please: cc the freesurfer list when answering
2011/2/22 Carolina Valencia cvalencia@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 ppj@netfilter.com.br
run this command
sudo rm -rf $FREESURFER_HOME
2011/2/21 Carolina Valencia cvalencia@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 $FREESURFER_HOME
It says that I don't have permission,how I can unistall it, if i'm the admin user?
Thanks in advance,
Carolina
2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <ppj@netfilter.com.br
It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS
2011/2/21 Carolina Valencia cvalencia@linkdx.com.co
Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux
Thanks,
2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < ppj@netfilter.com.br>
Please send the result of the command:
uname -a
On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < cvalencia@linkdx.com.co> wrote:
> Hi Bruce, > > I'm experimenting problems with the installation on Ubuntu too. > There's is warning in the welcome message, it seems that something is > missing: > > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist > FREESURFER_HOME /home/cvalencia/Descargas/freesurfer > FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects > MNI_DIR /home/cvalencia/Descargas/freesurfer/mni > FSL_DIR /usr/share/fsl/4.1 > > > I try to test it and it shows > cvalencia@cvalencia-Precision-WorkStation-T3400:~$ 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 fischl@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. > >
--
--
Dear Pedro,
I would like to start with the tutorials but I don't have permission to copy the data to the subjects directory, how I can change this?
Best regards,
Carolina
2011/2/22 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br
try the command:
sudo apt-get install tcl
-- PPJ
Please: cc the freesurfer list when answering
2011/2/22 Carolina Valencia cvalencia@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 ppj@netfilter.com.br
run this command
sudo rm -rf $FREESURFER_HOME
2011/2/21 Carolina Valencia cvalencia@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 $FREESURFER_HOME
It says that I don't have permission,how I can unistall it, if i'm the admin user?
Thanks in advance,
Carolina
2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < ppj@netfilter.com.br>
It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS
2011/2/21 Carolina Valencia cvalencia@linkdx.com.co
Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux
Thanks,
2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < ppj@netfilter.com.br>
Please send the result of the command: > > uname -a > > > On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < > cvalencia@linkdx.com.co> wrote: > >> Hi Bruce, >> >> I'm experimenting problems with the installation on Ubuntu too. >> There's is warning in the welcome message, it seems that something >> is missing: >> >> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist >> FREESURFER_HOME /home/cvalencia/Descargas/freesurfer >> FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii >> SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects >> MNI_DIR /home/cvalencia/Descargas/freesurfer/mni >> FSL_DIR /usr/share/fsl/4.1 >> >> >> I try to test it and it shows >> cvalencia@cvalencia-Precision-WorkStation-T3400:~$ 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 fischl@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@nmr.mgh.harvard.edu
-
Carolina Valencia -
Pedro Paulo de Magalhães Oliveira Junior