Hi All,
I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying:
[freesurfer home path]/mri_convert: Exec format error. Binary file not executable
It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks,
Nathan
what version did you download?
Nathan Dankner wrote:
Hi All,
I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying:
[freesurfer home path]/mri_convert: Exec format error. Binary file not executable
It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I downloaded version 5, and installed it into my home directory, as opposed to user/local... I don't know if that's an issue or not
On Thu, Dec 2, 2010 at 4:43 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
what version did you download?
Nathan Dankner wrote:
Hi All,
I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying:
[freesurfer home path]/mri_convert: Exec format error. Binary file not executable
It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Can you be more specific? Which file in particular? We have different distributions for different platforms. If you downloaded one that does not match your platform then it will generate that error.
doug
Nathan Dankner wrote:
I downloaded version 5, and installed it into my home directory, as opposed to user/local... I don't know if that's an issue or not
On Thu, Dec 2, 2010 at 4:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what version did you download? Nathan Dankner wrote: Hi All, I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying: [freesurfer home path]/mri_convert: Exec format error. Binary file not executable It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks, Nathan ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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.
Oh sorry. I downloaded the CentOS 64-bit linux file, which should match my platform...
On Thu, Dec 2, 2010 at 5:06 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Can you be more specific? Which file in particular? We have different distributions for different platforms. If you downloaded one that does not match your platform then it will generate that error.
doug
Nathan Dankner wrote:
I downloaded version 5, and installed it into my home directory, as opposed to user/local... I don't know if that's an issue or not
On Thu, Dec 2, 2010 at 4:43 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what version did you download?
Nathan Dankner wrote:
Hi All, I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying: [freesurfer home path]/mri_convert: Exec format error. Binary file not executable It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks, Nathan
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Can you send the result of cat $FREESURFER_HOME/build-stamp.txt
Nathan Dankner wrote:
Oh sorry. I downloaded the CentOS 64-bit linux file, which should match my platform...
On Thu, Dec 2, 2010 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you be more specific? Which file in particular? We have different distributions for different platforms. If you downloaded one that does not match your platform then it will generate that error. doug Nathan Dankner wrote: I downloaded version 5, and installed it into my home directory, as opposed to user/local... I don't know if that's an issue or not On Thu, Dec 2, 2010 at 4:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: what version did you download? Nathan Dankner wrote: Hi All, I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying: [freesurfer home path]/mri_convert: Exec format error. Binary file not executable It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks, Nathan ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Hi Doug,
Sorry for being slow in responding. Here's the output of the command:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
when I call the uname -m command I don't get an output of x86_64, however. It comes up as i686...
On Thu, Dec 2, 2010 at 5:34 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Can you send the result of cat $FREESURFER_HOME/build-stamp.txt
Nathan Dankner wrote:
Oh sorry. I downloaded the CentOS 64-bit linux file, which should match my platform...
On Thu, Dec 2, 2010 at 5:06 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you be more specific? Which file in particular? We have different distributions for different platforms. If you downloaded one that does not match your platform then it will generate that error.
doug
Nathan Dankner wrote:
I downloaded version 5, and installed it into my home directory, as opposed to user/local... I don't know if that's an issue or not On Thu, Dec 2, 2010 at 4:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: what version did you download? Nathan Dankner wrote: Hi All, I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying: [freesurfer home path]/mri_convert: Exec format error. Binary file not executable It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks, Nathan
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
That's the problem. You have a 32 bit machine but trying to run a 64 bit program. I think there should be a 32bit version of FS on the distribution page.
doug
Nathan Dankner wrote:
Hi Doug,
Sorry for being slow in responding. Here's the output of the command:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
when I call the uname -m command I don't get an output of x86_64, however. It comes up as i686...
On Thu, Dec 2, 2010 at 5:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the result of cat $FREESURFER_HOME/build-stamp.txt Nathan Dankner wrote: Oh sorry. I downloaded the CentOS 64-bit linux file, which should match my platform... On Thu, Dec 2, 2010 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Can you be more specific? Which file in particular? We have different distributions for different platforms. If you downloaded one that does not match your platform then it will generate that error. doug Nathan Dankner wrote: I downloaded version 5, and installed it into my home directory, as opposed to user/local... I don't know if that's an issue or not On Thu, Dec 2, 2010 at 4:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: what version did you download? Nathan Dankner wrote: Hi All, I've just installed freesurfer onto a linux node, and immediately encountered a problem when trying to run my first scan. After executing the recon-all command, the terminal spits out a string of errors saying: [freesurfer home path]/mri_convert: Exec format error. Binary file not executable It does this for every binary which is called upon executing recon-all and exits with errors. Any idea what's wrong? Thanks, Nathan ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Nathan Dankner