External Email - Use Caution
The default path you show me is exactly what I want! Thank you!
Kiyotaka
On Tue, Jul 20, 2021 at 8:23 PM fsbuild <fsbu...@contbay.com> wrote:
> 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 <kiyot...@nemotos.net> wrote:
>
> 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
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1-DJfjJ2ump0OIrxymCZSJDyWjZ1lRUvfVbh_ALmAvflMUcQ4VbQ-rL8qJZ0CNb57YXcyvUNZBuhzNh2CljpXlJZdUE4zJ7_HWwyNWe6w5P5lT04JOCA8D6_d6HPz650QPv_q0r0-NzSCNXmkR0zvs0ELVekUvBL7SEvG3dP3RbqqeQYQ1ueLz9aKEiv-uWJ0VvFL3MBCAWtACdr-2-N8_C7zdglQcacc4rnBkvgL-jGlj1FTeHA7FFGrhOZMcnHHCcIVgLdtTsJAB27liidlKA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>>> <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
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web..cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1oR4zTJZ2lVLFIwnQAtra7UnECDPxfw3hqF25fYdo6zKFHc_a6M6izJUc2_TCw1rqC8FLRSpLtuggsv2PwOpJDpfE-zd1d3U58SHAORDFfu77BUPdfKFSGglNxqkKm7M7kTrq8Y-6pUocGp_nQwMUhgvIZNcjBcfSWkGbwEP2fSnfvC-4mTp7I3yNzM8pEVm24_W7EjspUEZLZErtG5yGadZrULcO0DY2HNPQ_mfFP_uSFGkh6vS4Oe5TRjc89TlrVcCJVsc4TFDM2ZlhMfnblg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>> <https://secure-web.cisco.com/160o86r0Wg5hAWXbUcGcJ_MNRJJoO9nSvvvdSf0RIWdKuZ60guHgPYdDLMWPLctFsmW8v2_W95fIQKEHtdEZoiuWj0FAFY7moIi_xp1H2fdyrRQURKgGXVkHwc2JFPcFhA9prmc4ZzBrrpb-iyq-pFoQRjufitZHAj3jtpCeIXoYBgXB2ODwVkiPK1PeBJqZf5KaW7LXbZ184ROm5g3oAAn-Aiy0Iai2Z5l3tBKnd5cJcqGiLA2Gw7hYSueg8L3hfVMOjhR_JvOcbMZN1p4dbbw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>> The information in this e-mail is intended only for the person to whom
>>> it is addressed. If you believe this e-mail was sent to you in error and
>>> the e-mail contains patient information, please contact the Mass General
>>> Brigham Compliance HelpLine at *MailScanner has detected a possible
>>> fraud attempt from "secure-web.cisco.com" claiming to be*
>>> http://secure-web.cisco.com/1axpjxhWc6SvbPdKOY-UmC7uBCS0StHPYkbxqdwb-7_EZ-SQaqhmPkI-xOkMWnHtW0v3aGyXD8T2WPYrbWXOlVrvhVarNlSL-oSIadc_sECzU6LAKS1hup7jbYmrVWDhT6UCCnrnZtEAE7-vSSDAKQ1mfBVcvRbO7qM4THRLi33XM17-E4o3RKfRepasu1LFmtcVjCMgAMkkhH8X_xkPgkTAA8HkIFN0kzv92SHYfYblH6UVLOfL0ZgSJZt_4SxV4igukAcn-cFz0wJ-I6ZjmwQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>> <http://secure-web.cisco.com/1sNbeEVtvuwqzKlXCpXC5oSagM47ENvIzIX1rje6hMrQRa0xr50lz9ftON5MKtxQ7KzUyGjFY4HQBMsg7Lfc9e6XDe7wmpXz8mgYsRTZQgO7dDQv5v0oyM6eXaFUdPe756rkK6nv1j__R8miVAPj503r7RtesN2CMzfuTvi-gVhpYtEx07MUELh2MbMAxKgvKAN7xbaW7spFL1xcXNOMq8FHW0USHm_8Lp0MfDVArOACMzjeUZ4iaCTY9fTuQUJnbOOmQRyIuaqKYpeQ3Ao4Eqw/http%3A%2F%2Fwww..massgeneralbrigham.org%2Fcomplianceline>
>>> . If the e-mail was sent to you in error but does not contain patient
>>> information, please contact the sender and properly dispose of the e-mail.
>>> Please note that this e-mail is not secure (encrypted). If you do not
>>> wish to continue communication over unencrypted e-mail, please notify the
>>> sender of this message immediately. Continuing to send or respond to
>>> e-mail after receiving this message means you understand and accept this
>>> risk and wish to continue to communicate over unencrypted e-mail.
>>>
>>>
>>
>> --
>> 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
>> _______________________________________________
>> Freesurfer mailing list
>> freesur...@nmr.mgh.harvard..edu <Freesurfer@nmr.mgh.harvard.edu>
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1oR4zTJZ2lVLFIwnQAtra7UnECDPxfw3hqF25fYdo6zKFHc_a6M6izJUc2_TCw1rqC8FLRSpLtuggsv2PwOpJDpfE-zd1d3U58SHAORDFfu77BUPdfKFSGglNxqkKm7M7kTrq8Y-6pUocGp_nQwMUhgvIZNcjBcfSWkGbwEP2fSnfvC-4mTp7I3yNzM8pEVm24_W7EjspUEZLZErtG5yGadZrULcO0DY2HNPQ_mfFP_uSFGkh6vS4Oe5TRjc89TlrVcCJVsc4TFDM2ZlhMfnblg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1PYiesaHKg39fdFzcC9TO5yhVmP-Xs-yLSKdCzx2VNakVmXJ72isb5oLqAXFUNiSj5TXQAstSGFJGGckVErjK88y985R-IhGoOrwD9qO96gRmOd_38kC6E1nR9QgY5E_uIEu36a3bxQ5Zpl7ozmE7HkzeePinGoSfZG2Tw9b7wv0g3H0S5ds-4CY14mCPWCrKmEVaKRaqGQIDok6efJXXNyFcdcYyQe4Rr-X9fG-Emt6Ap8R83dvzdEtxaj85urDrtU7NplCWTFGERO_mrZ8fEw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1oR4zTJZ2lVLFIwnQAtra7UnECDPxfw3hqF25fYdo6zKFHc_a6M6izJUc2_TCw1rqC8FLRSpLtuggsv2PwOpJDpfE-zd1d3U58SHAORDFfu77BUPdfKFSGglNxqkKm7M7kTrq8Y-6pUocGp_nQwMUhgvIZNcjBcfSWkGbwEP2fSnfvC-4mTp7I3yNzM8pEVm24_W7EjspUEZLZErtG5yGadZrULcO0DY2HNPQ_mfFP_uSFGkh6vS4Oe5TRjc89TlrVcCJVsc4TFDM2ZlhMfnblg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
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