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While it does not currently work to change the default install path, that default install path for the .deb (and .rpm) 7.2.0 installer files is /usr/local/freesurfer/7.2.0 (which reads like the path you want to use).

If you already have different releases under /usr/local/freesurfer/<rev> that are not rev=7.2.0, e.g. from using the tar files (as this is the first .deb package), then the packaging tools won’t know anything about them and should not touch them when installing 7.2.0.  Or apt install and apt remove will only affect /usr/local/freesurfer/7.2.0 with the freesurfer_7.2.0_amd64.deb package.

Still looking into nu_correct.

- R.

On Jul 20, 2021, at 06:21, Kiyotaka Nemoto <kiyotaka@nemotos.net> wrote:

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Hello R,

Thank you for letting me know that the deb file is now available. It's so useful for Ubuntu users to install FreeSurfer using the deb file.
Can I ask you one more question? Can I specify the install directory using the deb file?
I manage different versions of FreeSurfer by installing under /usr/local/freesurfer/{6.0.1, 7.1.1, 7.1.2}.
If I can specify the directory, then I would love to use the deb file.

As for the missing mni directory, I'm concerned about nu_correct.
In my understanding, recon-all still uses nu_correct as default unless we set DoAntsN3 or DoAntsN4.
nu_correct is located under $FREESURFER_HOME/mni/bin, so I thought it might be missed for some reason.

Best regards,

Kiyotaka



On Tue, Jul 20, 2021 at 3:32 PM fsbuild <fsbuild@contbay.com> wrote:
Hello Kiyotaka,

You may not need to be concerned about that warning.  You can suppress it by setting the following in your shell environment.

$ export NO_MINC=1

For Ubuntu linux, if you have sudo/root/admin privileges, then you could try running the installer file instead of using the tar file, i.e.,

$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb

- R.

On Jul 19, 2021, at 21:08, Kiyotaka Nemoto <kiyotaka@nemotos.net> wrote:

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Dear Doug,

Thank you for the announcement of 7.2.0 update.
I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that the 'mni' directory is missing.

As a result, now the shell shows warning about MNI

=====
-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.2.0
FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /home/username/freesurfer/7.2.0/subjects
WARNING: MINC_BIN_DIR not defined.
         'nu_correct' and other MINC tools
         are used by some Freesurfer utilities.
         Set NO_MINC to suppress this warning.
WARNING: MINC_LIB_DIR not defined.
         Some Freesurfer utilities rely on the
         MINC toolkit libraries.
         Set NO_MINC to suppress this warning.
FSL_DIR           /usr/local/fsl
=====


Is it intended?

Best regards,

Kiyotaka



On Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
We are  please to announce version 7.2. Mostly bug fixes and 
behind-the-scenes enhancements. But there are a few new goodies and one 
new "known issue" about defacing. Check out
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
doug


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-- 
Kiyotaka Nemoto, M.D., Ph.D.
Associate Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: kiyotaka@nemotos.net
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