no, because I don't know what the volume are that you are usingOn Wed, 19 Nov 2014, Gunjan Gautam wrote:
Ok I try this out.
Did you answer my Query 1(related to cropped output of mri_convert command ?
I probably did not understand.
On Nov 19, 2014 8:10 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
Hi Gunjan
FreeSurfer 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
>
> >
>
> >
>
> >
>
> >
_______________________________________________
>
> >
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
_______________________________________________
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.
