Do I need to run the SetupFreeSurferEnv.csh every time before I start the Freesurfer? I thought it is only for initial intallation? PS: even after I run the SetupFreeSurferEnv.csh when i installed Freesurfer the other day, it showed -------- 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 /ho me/jie/Documents/freesurfer//mni But it did not work for the test "tkmedit bert orig.mgz"; it reponded“Illegal instruction” Any suggestion for the problem? Thanks Jie
> From: ni...@nmr.mgh.harvard.edu > To: remembe...@hotmail.com > Date: Sat, 26 Feb 2011 18:30:31 -0500 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] installation problem > > the SetupFreeSurferEnv.csh file needs to be run. see installation > instructions: > > http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration > > n. > > On Fri, 2011-02-25 at 08:25 +0800, Liukarl wrote: > > Hello, Nick > > > > I tried mri_convert work, glxgears,tksurfer, qdec,freeview. It all > > respond as "Command not found" > > > > two questions: > > > > 1) How should I initiate freesufter evey time i turn on the computer? > > > > 2) The other day when I installed freesurfer,i typed “tkmedit bert > > orig.mgz”, it reponded “Illegal instruction”. If I typed in > > “recon-all”, it showed > > “ Required Arguments: > > -subjid <subjid> > > -<process directive>…... ” > > > > and the other arguments. > > > > But when i tried the “recon-all” today, it said "Command not found". > > > > Another thing is i installed the freesurfer in my Document folder, > > instead of the local folder. Although i am the administrator, Ubuntu > > would not allow me to move any file to the local folder.. > > > > Any idea of the problem of freesurfer in my computer? > > > > thanks > > > > Jie > > > > > > > > > > > > > From: ni...@nmr.mgh.harvard.edu > > > To: remembe...@hotmail.com > > > Date: Wed, 23 Feb 2011 18:32:58 -0500 > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] installation problem > > > > > > does mri_convert work? > > > > > > glxgears? > > > > > > tksurfer? > > > > > > qdec? > > > > > > freeview? > > > > > > your installation should work on ubuntu, as it has for other people, > > so > > > i'm a bit at a loss. > > > > > > n. > > > > > > On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote: > > > > Hello, Nick > > > > > > > > the output of uname -a is > > > > > > > > "Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21 > > > > 17:40:48 UTC 2011 i686 GNU/Linux" > > > > > > > > thanks > > > > > > > > Jie > > > > > > > > > > > > > > > > > > > > > Subject: Re: [Freesurfer] installation problem > > > > > From: ni...@nmr.mgh.harvard.edu > > > > > To: remembe...@hotmail.com > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > Date: Wed, 23 Feb 2011 11:59:16 -0500 > > > > > > > > > > what is the output of > > > > > > > > > > uname -a > > > > > > > > > > > > > > > On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote: > > > > > > Hello, Freesurfer experts: > > > > > > > > > > > > > > > > > > > > > > > > I emailed some installation problems a couple days ago, but > > > > haven’t > > > > > > answered yet. 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 /ho me/jie/Documents/freesurfer//mni > > > > > > > > > > > > > > > > > > > > > > > > Everything seems fine and I also added the .license file to > > the< > > > > br>> > 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! > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > PS: my Ubuntu is 32-bit and choose the 32-bit version > > Freesurfer. > > > > > > > > > > > > > > > > > > > > > > > > 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 i nformation, 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 > > _______________________________________________ > 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 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.
