Hi Gunjan
just run recon-all and it will do everything that we know how to do
(including those steps)
cheers
Bruce
On Wed, 19 Nov 2014, Gunjan Gautam wrote:
Ok, I try this tomorrow morning.
I will be thankful if you could tell me about getting brain mask and
performing skull stripping otherwise I'll have to wait for 12 hours to get
your replies as our working hours doesn't match.
On Nov 18, 2014 8:45 PM, "Z K" <zkauf...@nmr.mgh.harvard.edu> wrote:
Gunjan, this may be related to an Ubuntu specific issue we
address on
the Freesurfer download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Specifically the part thats states the following:
***
On Ubuntu, you might have to do this if qdec or freeview
complain about
libjpeg or libtiff:
cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu
distros)
sudo ln -s libjpeg.so.8 libjpeg.so.62
sudo ln -s libtiff.so.4 libtiff.so.3
***
-Zeke
On 11/18/2014 03:55 AM, 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
> <mailto: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>
> > <mailto: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>>
> > > <mailto: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>>
> > <mailto: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
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> > > dispose of the e-mail.
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> > >
> > > _______________________________________________
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >
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> > >
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> <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>
> >
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
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