External Email - Use Caution
Hello Michael,
Point taken. The issue with the exclusion of files under the ./mni
directory did not change any source code and no binaries were
re-compiled. The timestamps did change on all the files listed under
https://secure-web.cisco.com/1gf9Oci5MYp5_O9OPy-mYs2llFtxC9m8cZj1-QcwGNtoFN6yTjwwZZLTe7WUdiUu0jUaJI1InHtD9k3CTTyQJ0zmQSVOdJaTnjYPkLZvnTPBBniIAXC7IF7OVZ1BYArZOH5DNX9m2qTxatuTa4rOel3mexPhs2fhxS_v9lGmB0S5F4Rb4EintdErONFoeSqd1WhzeVHY5ZJSttrw6BC_zOz9C6151rIBrdW8mXqt_7l1o4rdVa8ebmGosW3KfbGp6kCXOHsadnvWrfxpbrTFioQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%26nbsp;
- R.
Michael Krause (kra...@mpib-berlin.mpg.de) August 12,
2021 at 06:59
External Email - Use Caution
Hi,
I just found this post and it explains why I'm seeing this:
$ ls -lrt freesurfer-linux-centos6_x86_64-7.2.0.tar.gz*
-rw-r--r-- 1 krause domain users 4917297770 Jul 15 13:05
freesurfer-linux-centos6_x86_64-7..2.0.tar.gz
-rw-r--r-- 1 krause domain users 5012301197 Jul 21 08:13
freesurfer-linux-centos6_x86_64-7.2.0.tar.gz.1
$ md5sum freesurfer-linux-centos6_x86_64-7.2.0.tar.gz*
cac0f97a4034c3c234fdbe99707d7d93 freesurfer-linux-centos6_x86_64-7.2.0.tar.gz
eae2d09b063794bf2c8ed3e50ee80bd8
freesurfer-linux-centos6_x86_64-7.2.0.tar..gz.1
$ tar tf freesurfer-linux-centos6_x86_64-7.2.0.tar.gz..1
freesurfer/mni/bin/mritotal
freesurfer/mni/bin/mritotal
$ tar tf freesurfer-linux-centos6_x86_64-7.2.0.tar.gz
freesurfer/mni/bin/mritotal
tar: freesurfer/mni/bin/mritotal: Not found in archive
tar: Exiting with failure status due to previous errors
Can I say that, as a sysadmin / package maintainer, I find this a little
unfortunate. There is no way for me to know that I had to get a new tar
ball, because the version number stayed exactly the same :( It's just that I
found this post *after* we stumbled over an issue with the missing MNI
directory.
best regards
Michael
fsbuild (fsbu...@contbay.com) July 21, 2021 at 14:20
External Email - Use
Caution Hello Kiyotaka,
Please try refreshing your copy/install of the Ubuntu 7.2.0
distribution as the packages have been updated to fix the warning below.
I think you were using the installer, so you could try the commands
below to download and re-install with apt. (If you were using the tar
file then just change the file name in the wget command to be
freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz, expand it in the right
location and skip the commands with sum, apt remove, apt install).
..... with installer ....
$ rm -f freesurfer_7.2.0_amd64.deb
$ wget
https://secure-web.cisco.com/1-sNHs519XorwwEeem0CCMvXVsMABHYYE70Coq941BKBnOblzFlYhPvNKfMPh5YtJ3p_nRc05UlLYv5Zu0ogpQb4CQU9EzTkHn6uPG9AECc6JuHRFrHSP8sVJZlTtSHymaruImVGrc5dW6uWLiLCbo15T4DcURQZtigjYiasBgz1hycLHX3eMkssq06JBZtCdGzJEPECsoHz0ukqCkrqNcLjap7MovbzpJBJZo9R7e-SePuh2JhlDxf6UPmBiPXYVKXsPIKWdxP3isyFiiwmcoA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer_7.2.0_amd64.deb
$ sum freesurfer_7.2.0_amd64.deb
20191 3199044
$ sudo apt remove freesurfer
..... output deleted ...
$ apt install ./freesurfer_7.2.0_amd64.deb
..... output deleted ...
..... check environment ...
$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0
$ source $FREESURFER_HOME/SetUpFreeSurfer..sh
..... the output should have no warnings and you can also check ...
$ env | grep MINC
MINC_BIN_DIR=/usr/local/freesurfer/7.2.0/mni/bin
MINC_LIB_DIR=/usr/local/freesurfer/7.2.0/mni/lib
$ which nu_correct
/usr/local/freesurfer/7.2.0/mni/bin/nu_correct
- R.
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