Re: [Freesurfer] installation problem in ubuntu
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 > try the command: > > sudo apt-get install tcl > > -- PPJ > > Please: cc the freesurfer list when answering > > 2011/2/22 Carolina Valencia > > 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 >> >>> run this command >>> >>> sudo rm -rf $FREESURFER_HOME >>> >>> >>> >>> 2011/2/21 Carolina Valencia >>> Thanks Pedro, How I uninstall that version to re-install the correct version? I look for some answers and try rm -rf $FREESURFER_HOME It says that I don't have permission,how I can unistall it, if i'm the admin user? Thanks in advance, Carolina 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < p...@netfilter.com.br> > It seems you are running the 64-bit version of FreeSurfer in a 32-bit > OS > > > 2011/2/21 Carolina Valencia > > >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae >> #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux >> >> Thanks, >> >> >> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < >> p...@netfilter.com.br> >> >> Please send the result of the command: >>> >>> uname -a >>> >>> >>> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < >>> cvalen...@linkdx.com.co> wrote: >>> Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ 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 > 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 >> $FREESURFER_HOME/SetUpFreeSurfer.sh” >> >> >> >> >> freesurfer-Linux-centos4-stable-pub-v5.0.0 >> >> Setting up environment for >> FreeSurfer/FS-FAST (and FSL) >> >> FREESURFER_HOME >> /home/jie/Documents/freesurfer/ >> >> FSFAST_HOME >> /home/jie/Documents/freesurfer//fsfast >> >> FSF_OUTPUT_FORMAT nii >> >> SUBJECTS_DIR >> /home/jie/Documents/freesurfer//subjects >> >> MNI_DIR >> /home/jie/Documents/freesurfer//mni >> >> >> >> >> Everything seems fine and I also added >> the .license file to the freesurfer folder. >> >> >> >> But when I test it by “tkmedit bert >> orig.mgz”, it reponds “Illegal instruction” >> >> >> >> If I type in “recon-all”, it will >> show >> >> “
Re: [Freesurfer] installation problem in ubuntu
try the command: sudo apt-get install tcl -- PPJ Please: cc the freesurfer list when answering 2011/2/22 Carolina Valencia > Hi Pedro, > > Finally, I could install it with the license file and the environment is > properly set without warnings. > But trying to test it, following the instruction on the wiki page I have a > problem > > cvalencia@cvalencia-Precision-WorkStation-T3400:~$ 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 > >> run this command >> >> sudo rm -rf $FREESURFER_HOME >> >> >> >> 2011/2/21 Carolina Valencia >> >>> Thanks Pedro, >>> >>> How I uninstall that version to re-install the correct version? >>> I look for some answers and try >>> >>> rm -rf $FREESURFER_HOME >>> >>> It says that I don't have permission,how I can unistall it, if i'm the >>> admin user? >>> >>> Thanks in advance, >>> >>> Carolina >>> >>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior >> > >>> It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia > Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae > #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux > > Thanks, > > > 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < > p...@netfilter.com.br> > > Please send the result of the command: >> >> uname -a >> >> >> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < >> cvalen...@linkdx.com.co> wrote: >> >>> Hi Bruce, >>> >>> I'm experimenting problems with the installation on Ubuntu too. >>> There's is warning in the welcome message, it seems that something is >>> missing: >>> >>> freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist >>> FREESURFER_HOME /home/cvalencia/Descargas/freesurfer >>> FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast >>> FSF_OUTPUT_FORMAT nii >>> SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects >>> MNI_DIR /home/cvalencia/Descargas/freesurfer/mni >>> FSL_DIR /usr/share/fsl/4.1 >>> >>> >>> I try to test it and it shows >>> cvalencia@cvalencia-Precision-WorkStation-T3400:~$ 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 >>> 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 > > -…... > ” > 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@nm
Re: [Freesurfer] installation problem in ubuntu
run this command sudo rm -rf $FREESURFER_HOME 2011/2/21 Carolina Valencia > Thanks Pedro, > > How I uninstall that version to re-install the correct version? > I look for some answers and try > > rm -rf $FREESURFER_HOME > > It says that I don't have permission,how I can unistall it, if i'm the > admin user? > > Thanks in advance, > > Carolina > > 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior > >> It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS >> >> >> 2011/2/21 Carolina Valencia >> >> >>> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae >>> #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux >>> >>> Thanks, >>> >>> >>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior >> > >>> >>> Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < cvalen...@linkdx.com.co> wrote: > Hi Bruce, > > I'm experimenting problems with the installation on Ubuntu too. > There's is warning in the welcome message, it seems that something is > missing: > > freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 > Setting up environment for FreeSurfer/FS-FAST (and FSL) > WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist > FREESURFER_HOME /home/cvalencia/Descargas/freesurfer > FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects > MNI_DIR /home/cvalencia/Descargas/freesurfer/mni > FSL_DIR /usr/share/fsl/4.1 > > > I try to test it and it shows > cvalencia@cvalencia-Precision-WorkStation-T3400:~$ 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 > >> 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 >>> >>> -…... >>> ” >>> 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 Compl
Re: [Freesurfer] installation problem in ubuntu
It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia > > 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 > > Please send the result of the command: >> >> uname -a >> >> >> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia > > 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 >>> 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 > > -…... > ” > 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
Re: [Freesurfer] installation problem in ubuntu
Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia 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 > >> 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 >>> >>> -…... >>> ” >>> 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.
Re: [Freesurfer] installation problem in ubuntu
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 > 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 >> >> -…... >> ” >> 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.
Re: [Freesurfer] installation problem in ubuntu
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 -¡... ¡± 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] installation problem in ubuntu
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 -…... ” 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.
