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Hello Developers,
I am attempting to build Freesurfer from source on my Ubuntu 18.04.1 LTS machine. I have followed the instructions on the freesurfer_linux_developershttp://freesurfer.net/fswiki/freesurfer_linux_developers_page wiki, and have successfully gotten through steps 1 and 2. However, when trying to install the third party dependencies at step 3 via wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz, I get the following response:
~$ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz --2018-10-30 21:25:16-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz => ‘centos6-x86_64-packages.tar.gz’ Resolving surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ (surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/)... 132.183.240.105 FreeSurferhttp://surfer.nmr.mgh.harvard.edu/ surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration
FreeSurferhttp://surfer.nmr.mgh.harvard.edu/ surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration
Connecting to surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ (surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/)|132.183.240.105|:21... connected. FreeSurferhttp://surfer.nmr.mgh.harvard.edu/ surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration
FreeSurferhttp://surfer.nmr.mgh.harvard.edu/ surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration
Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/dist/fs_supportlibs/prebuilt/centos6_x86_64 ... No such directory ‘pub/dist/fs_supportlibs/prebuilt/centos6_x86_64’.
I looked in the pub/dist directory and there is no folder named ‘fsl_supportlibs’. I found a file ‘freesurfer-linux-centos6_x86_64-dev.tar.gz’ in the folder pub/dist/freesurfer/dev/‘ but I’m not sure if this contains the third party dependencies and did not want to download without knowing.
I do not have build-stamp.txt file in my $FREESURFER_HOME to provide you with the freesurfer version, but I am using the current version on the github repo (although that shouldn’t matter for this issue).
Do you have any advice? I couldn’t find any similar issues in the archives, and the wiki says it was last updated this past September, so I believe it is still a current wiki.
Thank you! Christian McDaniel
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Christian McDaniel President, Deep Learning @ UGA Data Scientist, UGA CVIOG ITOS Data Analytics Team Master’s Student, Institute for Artificial Intelligence Boyd GSRC University of Georgia Athens, GA