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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
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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.
