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
> >
> >
> >
> >
_______________________________________________
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> > Freesurfer@nmr.mgh.harvard.edu
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> <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
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the e-mail was
sent to
> > you in error
> > but does not contain patient
information, please contact
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> > and properly
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> >
> >
> >
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> >
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> >
>
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_______________________________________________
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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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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.
