Hi Gunjan
if you are using bash, you need to run the instructions for bash at:
http://freesurfer.net/fswiki/SetupConfiguration
for example, it says:
If using bash or sh, type:
export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
cheers
Bruce
On
Tue,
18 Nov 2014, Gunjan Gautam wrote:
I followed the installation process from
http://freesurfer.net/fswiki/LinuxInstall.
while running "setenv FREESURFER_HOME /usr/local/freesurfer" it shows that
setenv command not found.
Is it necessary to place FreeSurfer directory in to /usr/local ? I have it
on my desktop.
On Tue, Nov 18, 2014 at 6:47 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
I think if the file existed you would have gotten a syntax
error. Does it exist? If not, then either you didn't install
FreeSurfer there or something went wrong with your installation
cheers
Bruce
On Tue, 18 Nov 2014, Gunjan Gautam wrote:
I ran but its showing error like below:
bibl04@BIBL04:~/Desktop/freesurfer$ source
/Desktop/freesurfer/SetUpFreeSurfer.csh
bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No
such file or directory
May be due to the shell. What should I do now?
On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Gunjan
FREESURFER_HOME should be an environment
variable, not the name
of a directory. It should point to the
directory that you
installed FreeSurfer in. You should run:
source <installation
directory>/SetUpFreeSurfer.csh
before trying to run anything
cheers
Bruce
On Tue, 18 Nov 2014, Gunjan Gautam wrote:
Hello Sir,
I have place the "license.txt" in the
same directory
that contains
build-stamp.txt as there were no
directory with name
"FREESURFER_HOME".
freeview command is not working and
showing below
message
"freeview.bin: error while loading
shared libraries:
libjpeg.so.62: cannot
open shared object file: No such file or
directory".
What next I need to do in order to
generate a output
brain mask.
Best Regards,
Gunjan
On Thu, Nov 13, 2014 at 12:24 AM, Z K
<zkauf...@nmr.mgh.harvard.edu> wrote:
Im having a little difficulty
following all
the avenues of your
attempts
to get this working, but the
bottom line is
that the error
message below
is complaining that you do not
have a valid
license file.
You need to go to this page and
register and
get the valid
license file:
https://surfer.nmr.mgh.harvard.edu/registration.html
Once you get a valid license file
you will
need to place it in
your
$FREESURFER_HOME directory (the
same directory
that contains
build-stamp.txt) and give it the
name .license
or license.txt.
Try both.
-Zeke
On 11/12/2014 01:29 PM, Gunjan
Gautam wrote:
> Sir earlier I was trying to use
FreeSurfer
using Virtual Box
in my
> Windows machine. There the
mri_convert
command did not work so
I
> switched to a Linux machine.
Now, I'm using
centos6_x86_64
version as my
> machine has the Ubuntu 12.04
platform and
here also facing the
same
> problem.
>
> I want to share one thing that
in my
institute I tried hard to
download
> FreeSurfer but every time it
resulted into a
time-out
situation so I had
> to ask someone to get it
downloaded and send
me through Google
drive.
> This was how I installed it in
my system.
>
> Best regards,
> Gunjan
>
> On Nov 12, 2014 9:15 PM, "Z K"
<zkauf...@nmr.mgh.harvard.edu
>
<mailto:zkauf...@nmr.mgh.harvard.edu>>
wrote:
>
> Gunjan,
>
> Are you using your own
version of
VirtualBox, with
freesurfer installed
> on it by you? Or the
VirtualBox version
of freesurfer made
by us and
> downloaded from our website?
I am
confused because in your
email below,
> freesurfer appears to be
installed on
the Desktop whereas
the
> prepackaged version made by
us is
installed in /usr/local
>
> -Zeke
>
> On 11/12/2014 08:54 AM,
Gunjan Gautam
wrote:
> > Hello Sir,
> >
> > License file is present
in the folder
but with the name
LICENSE.
> Should
> > I download it again ?
> >
> > Best Regards,
> > Gunjan
> >
> > On Nov 12, 2014 7:01 PM,
"Bruce
Fischl"
> <fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>
> >
<mailto:fis...@nmr.mgh.harvard.edu
>
<mailto:fis...@nmr.mgh.harvard.edu>>>
wrote:
> >
> > Hi Gunjan
> >
> > do you have a
license? If not you
need to download
and install it
> > (as noted in the
error message).
They are free.
> >
> > cheers
> > Bruce
> > On Wed, 12 Nov 2014,
Gunjan
Gautam wrote:
> >
> >
> > Hello Sir,
> >
> > I'm using
FreeSurfer through
Virtual Box. I
tried the below
> > command for
> > reslicing my
volume according
to a reference
volume but the
> > process gets
> > stuck at "
reading volume".
> >
> > mri_convert
A.nii.gz
A.resliced.nii.gz -rl
B.nii.gz
> >
> > A: Volume to be
resampled /
resliced
> > B: Reference
Volume
> >
> > Error message is
being shown
like below:
> >
> > mri_convert a.nii
a.resliced.nii -rl b.nii
> > $Id:
mri_convert.c,v
1.179.2.7 2012/09/05
21:55:16
> mreuter Exp $
> > reading from
a.nii...
> >
>
------------------------------__------------------------------__--------
-
-
----
> > ERROR: Invalid
FreeSurfer
license key found in
license file
> >
/home/bibl04/Data_Home/__Desktop/freesurfer/license.txt
> > If you are
outside the
NMR-Martinos Center,
> > go to
http://surfer.nmr.mgh.harvard.__edu
> >
<http://surfer.nmr.mgh.harvard.edu> to
> > get a valid
license file
(it's free).
> > If you are
inside the
NMR-Martinos Center,
> > make sure to
source the
standard
environment.
> >
> > Actually, I have
two volumes,
belong to the
same subject. One
> > volume is the
> > ground truth
which will be
considered as
standard for the
> second
> > volume
> > which is the
processed one or
the extracted
brain. To
> perform a
> > perfect
> > comparison
between both
volumes, these must
generate equal
> > number of slices
> > in order to
compare the
corresponding slide.
But here
> there is
> > problem with
> > my volumes, that
is while
performing slicing
Ground Truth
> volume is
> > generating 360
slice and
processed volume is
generating 181
> > slides. So
> > comparison can't
take place
in this way.
> >
> > What all I need
is to do the
resampling or
generating the 181
> > slides from
> > the Ground Truth
as well.
> >
> >
> > Best Regards,
> > Gunjan
> >
> >
> >
> >
_______________________________________________
> > Freesurfer mailing
list
> >
Freesurfer@nmr.mgh.harvard.edu
>
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
<mailto:Freesurfer@nmr.mgh.harvard.edu
>
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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 Partners
> Compliance
> > HelpLine at
> >
http://www.partners.org/complianceline . 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.
> >
> >
> >
> >
_______________________________________________
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> > Freesurfer@nmr.mgh.harvard.edu
>
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> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
>
_______________________________________________
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>
>
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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . 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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance
HelpLine at
http://www.partners.org/complianceline . 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.
_______________________________________________
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
