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-QcwGNtoFN6...;

- R.

Michael Krause (krause@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 (fsbuild@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-sNHs519XorwwEeem0CCMvXVsMABHYYE70Coq941BKBnOb...

$ 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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