External Email - Use Caution
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
$FREESURFER_HOME/mni/bin, so I thought it might be missed for some reason.Best
regards,KiyotakaOn Tue, Jul 20, 2021 at 3:32 PM fsbuild
<fsbu...@contbay.com> wrote:Hello Kiyotaka,You may not need to be
concerned about that warning. You can suppress it by setting the
following in your shell environment.$ export NO_MINC=1For 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/7.2.0FSFAST_HOME
/usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR
/home/username/freesurfer/7.2.0/subjectsWARNING: 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,KiyotakaOn 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 outMailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to
be https://secure-web.cisco.com/1BlHjRo1wiRb2WvddH8GfD4hFYtxGnnXI7YbPOxLLJtNiaE9mK4FbgdwrbDyo8oN8pEFz6RfSVHm0lB1H3_zII34LGJOcytt9Bn4tSC-41BMnzlgGvdx2hx7tKHrBB-K16eq4zmy1OtEnaqSLiuSomGG-9o4AXnLU_h1bCyPLpzlbQpJIZBfDedho0i0hBDanYP2WOPLMRyFin_OLQPTtayWCuxAEVTGahzpbwCXjVVz1ZEFQCPVS3o1T4StFAE79fLNplQjqPR2u9bsSXNje5A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotesdoug_______________________________________________Freesurfer
mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible
fraud attempt from "secure-web..cisco.com" claiming to
be https://secure-web.cisco.com/1z6kK1yL1k60FJGc27E2kn8x07SbszbMudIGBCb-M25TceJxiQ_UjpAPqAGws1aPBoKj8l9hJdOgS9thMsz0eyXaSKAtnzA7hiicXQFkiGUq_RUV4FKh5kE3Df3rv10vMHOsmpLITE8b-x-9pH9dXGMAj2H9io-yAXYzHxU-oGPT0MRZii_dzxBxZeBouagM5Et60Kcj1ldogkkYlm0P8OMRdBhwxtUuyCYS6pZf5OaZbJBoZi8kzR3jdyzxtji7VERIfwSDvJdwUldvPEytMmg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferThe
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/1O14LpmCbLrvsH2LqoMBFq1uWO82zk5EdVR0-IfqOoxWhWK_f_xyg81SkVJFX8XpckLNPJNcXvhsyvpeXSePetH2xCZGleoEL_LJPHVubEIUT2dhh9g9YMynaXoGBQ9Cu7tM6rNByqueiA4e3iKgJdd6YVwr8JgtsS0nUGUflJJ9WnBsTjsDsTELoM7JzFBDW3BoxnCLnoFcL-k6W9iiODqAIXC6Tr8iKSkqt0IbS8AQGTgmKh-T4W4kcB64Gc2b-3rgGci7F-_Pvl_phXLgezA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26nbsp;.
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 ProfessorDepartment
of PsychiatryDivision of Clinical Medicine, Faculty of MedicineUniversity of
Tsukuba1-1-1Tennodai Tsukuba, Ibaraki 305-8575,
JapanE-mail: kiyotaka@nemotos.net_______________________________________________Freesurfer
mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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