Re: [Freesurfer] Problems Installing Freesurfer on an EC2 AMI
Thanks for the suggestion with upx, Nick. I gave it a try and decompressed mri_info and mri_convert, but after decompressing neither worked and only returned a message of 'error' as the stdout. I also tried a 32 bit install on Ubuntu and an install on CentOS, and I am getting the same issue across the board. You are right about others running freesurfer on the amazon cloud (see https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018272.html), but I can't seem to find the freesurfer image mentioned in that thread in the amazon repository online. Does anyone have experience or had success with getting freesurfer running in the cloud? Cheers, Nolan On Wed, Aug 17, 2011 at 9:07 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: i havent seen this problem. i think others have run freesurfer on the amazon cloud before. the only thing i can think of, when you mention that the mri_* tools will not run (and in the recon-all.log, only the scripts printed their version info) is that the mri_* executables are all run through the UPX tool prior to distribution. this reduces their size, but maybe its having some weird effect on your system. if you have upx installed (Ultimate Packer for eXecutables), then you can run: upx -d mri_info to decompress mri_info (or mri_convert) then you might get some output when you run these commands. if so, then you would need to run upx -d on all the mri_* and mris_* executables. n. On Wed, 2011-08-17 at 20:50 -0700, Nolan Nichols wrote: Hello, I'm trying to install FreeSurfer (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) on an Ubuntu-10.04 x86_64 AMI hosted on Amazon's EC2, but after following the installation instructions I am unable to complete the Testing your Freesurfer Installation section. I am not trying to use any of the visualization tools, just recon-all -s bert -autorecon1 and the mri_tools, like mri_convert. I get the following error when I run recon-all -s bert -autorecon1 (recon-all.log attached) ... Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames ... I saw a previous post with the multi-frame error ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18444.html) and tried running mri_info to include in this email, but mri_info does not execute. Actually none of the mri_* tools are working and do not provide usage information when executed without any parameters. Any idea what I what I did wrong, or could this have to do with running freesurfer on EC2? Thanks for your help! Nolan ___ 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] Problems Installing Freesurfer on an EC2 AMI
Hello, I'm trying to install FreeSurfer (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) on an Ubuntu-10.04 x86_64 AMI hosted on Amazon's EC2, but after following the installation instructions I am unable to complete the Testing your Freesurfer Installation section. I am not trying to use any of the visualization tools, just recon-all -s bert -autorecon1 and the mri_tools, like mri_convert. I get the following error when I run recon-all -s bert -autorecon1 (recon-all.log attached) ... Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames ... I saw a previous post with the multi-frame error ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18444.html) and tried running mri_info to include in this email, but mri_info does not execute. Actually none of the mri_* tools are working and do not provide usage information when executed without any parameters. Any idea what I what I did wrong, or could this have to do with running freesurfer on EC2? Thanks for your help! Nolan recon-all.log Description: Binary data ___ 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] Problems Installing Freesurfer on an EC2 AMI
i havent seen this problem. i think others have run freesurfer on the amazon cloud before. the only thing i can think of, when you mention that the mri_* tools will not run (and in the recon-all.log, only the scripts printed their version info) is that the mri_* executables are all run through the UPX tool prior to distribution. this reduces their size, but maybe its having some weird effect on your system. if you have upx installed (Ultimate Packer for eXecutables), then you can run: upx -d mri_info to decompress mri_info (or mri_convert) then you might get some output when you run these commands. if so, then you would need to run upx -d on all the mri_* and mris_* executables. n. On Wed, 2011-08-17 at 20:50 -0700, Nolan Nichols wrote: Hello, I'm trying to install FreeSurfer (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) on an Ubuntu-10.04 x86_64 AMI hosted on Amazon's EC2, but after following the installation instructions I am unable to complete the Testing your Freesurfer Installation section. I am not trying to use any of the visualization tools, just recon-all -s bert -autorecon1 and the mri_tools, like mri_convert. I get the following error when I run recon-all -s bert -autorecon1 (recon-all.log attached) ... Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames ... I saw a previous post with the multi-frame error (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18444.html) and tried running mri_info to include in this email, but mri_info does not execute. Actually none of the mri_* tools are working and do not provide usage information when executed without any parameters. Any idea what I what I did wrong, or could this have to do with running freesurfer on EC2? Thanks for your help! Nolan ___ 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.
