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 /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!
PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer.
Jie
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 /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!
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
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: nicks@nmr.mgh.harvard.edu To: rememberer@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 /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!
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 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.
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: nicks@nmr.mgh.harvard.edu To: rememberer@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 /home/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 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.
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: nicks@nmr.mgh.harvard.edu To: rememberer@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: nicks@nmr.mgh.harvard.edu To: rememberer@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 /home/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 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 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:
How should I initiate freesufter evey time i turn on the computer?
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: nicks@nmr.mgh.harvard.edu To: rememberer@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: nicks@nmr.mgh.harvard.edu To: rememberer@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
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: nicks@nmr.mgh.harvard.edu To: rememberer@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:
How should I initiate freesufter evey time i turn on the computer?
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: nicks@nmr.mgh.harvard.edu To: rememberer@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: nicks@nmr.mgh.harvard.edu To: rememberer@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@nmr.mgh.harvard.edu
-
Liukarl -
Nick Schmansky