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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://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0 

- R.
Michael Krause (krause@mpib-berlin.mpg.de)
August 12, 2021 at 06:59
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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

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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://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer_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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