External Email - Use Caution
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 <fsbu...@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 <kiyot...@nemotos.net> wrote:
>
> External Email - Use Caution
>
> 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 <dgr...@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
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>> <https://secure-web.cisco.com/1Nq7OG4aqL5Xu5zmIj8jgt_aBH5sIzltmYEnh37LRCC02zUZJGtxhXjbr0RAoJKh7BtiL6-idjNjfiQdlADO4shk7DLtd9JwfjdpLzmw9--jn4lSaFUiwRrKjViNKHZQtQQPksweoYvQiKRJ-y0-kRCdPvOF3aK5lht5Pyc-LXUG4if3vb5foaGHGQb-9RCQhVi2Fen9Qpcz-5KsV8t2xasvxlBFP9nxk2X0URW-y0xEiEjnPng_y6WFgp42hIhMR-bF4VfXTbQTXEZX37XNcKg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>
>> doug
>>
>>
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>> The information in this e-mail is intended only for the person to whom it
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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: kiyot...@nemotos.net
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
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