Hi GunjanFreeSurfer has been designed to work as a pipeline. Picking out individual pieces and running them may or may not work, and certainly won't be as reliable. I would advise you to run recon-all -all, then you can use the contents of the subject directory to do whatever analyses you want (e.g. generate an un-bias-corrected, skull stripped volume).
The subject id is one that you make up - it will be the name of the directory under which the results are stored. Also specify a SUBJECTS_DIR on the command line, which will be the root directory under which all the individual subject trees live (with -sd <subjects directory path>
cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote:
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. This is the reason I used
mri_convert command.
If I am not wrong then recon-all command will do bias correction as well,
which is not my requirement. What I want is to have the binary brain mask
volume and brain volume only. recon-all command is asking for the subject-id
and I'm not sure about it. I have gone through its documentation but still
not able to run it properly. I request you to please help me in this.
Regards,
Gunjan
On Wed, Nov 19, 2014 at 6:50 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Gunjan
you need to give us more details. What are you trying to do? Why
not just run recon-all -all? That will be much easier than
trying to ru individual steps
chers
Bruce
On Wed, 19 Nov 2014, Gunjan Gautam wrote:
Hi,
I am facing few issues. I will be thankful if you
can help me out.
Query 1) I used "mri_convert a.nii a.resliced.nii
-rl b.nii" in order to
generate slices so that comparison may take place
properly. The command ran
properly but generating cropped slices.
I am attaching the input volume, reference volume
and the cropped slice
screenshot.
[icon_10_generic_list.png] a.nii
[icon_10_generic_list.png] b.nii
Query 2) For skull stripping I ran below command
bibl04@BIBL04:~/Desktop/freesurfer/bin$ recon-all
-i a.nii -autorecon1
and its showing error for subject id. I am really
not aware, what to write.
ERROR: must specify a subject id
Query 3) I did not find that which option from (1
to 31 ) should generate
the "binary brain mask".
Thanks,
Gunjan
On Wed, Nov 19, 2014 at 12:41 AM, Gunjan Gautam
<gunjan.gemin...@gmail.com>
wrote:
Ok, I go through that.
Thanks,
Gunjan
On Nov 19, 2014 12:37 AM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Gunjan,
it's all on the wiki. You should go
through our
tutorials
cheers
Bruce
On Wed, 19 Nov 2014, Gunjan Gautam
wrote:
Thank you
I will be thankful if you could
let me
know about the link related to
recon-all, in order to know about
the
parameters(input volume info etc)
associated to it and other usage.
On Nov 19, 2014 12:18 AM, "Bruce
Fischl"
<fis...@nmr.mgh.harvard.edu>
wrote:
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
> > >
> > >
> > >
> > >
_______________________________________________
> > >
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> > >
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>
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> >
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>
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>
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >
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<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> >
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> > >
> > >
> > >
The
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