I downloaded two volumes from BrainWeb database. One is treated as ground
truth because it has preassigned values(0-11) for each types of tissues and
by a simple coding binary brain mask can be achieved.
Another volume is the processed one using any brain extraction algorithm.
Now, I have two volum
Try swapping a and b. Or use mri_vol2vol with your reference volume as
target
On 11/19/14 7:41 AM, 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 th
Hi Gunjan
you need to give us more information. What are the two volumes? Why is
one "ground truth"? What in general are you trying to achieve?
cheers
Bruce
On Wed, 19
Nov 2014, Gunjan Gautam wrote:
I have attached both the volumes (reference and input) with my mail.
Its the last step of
I have attached both the volumes (reference and input) with my mail.
Its the last step of my work, I'm stuck at and not finding any solution. I
read that FreeSurfer can solve my problem.
I will be obliged if you find some time for this.
Best Regards,
Gunjan
On Nov 19, 2014 8:19 PM, "Bruce Fischl"
no, because I don't know what the volume are that you are using
On 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" wrote:
Hi G
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" wrote:
> Hi Gunjan
>
> FreeSurfer has been designed to work as a pipeline. Picking out individual
> pieces and running them may o
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 wan
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
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.
Ok, I go through that.
Thanks,
Gunjan
On Nov 19, 2014 12:37 AM, "Bruce Fischl" 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
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
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" wrote:
> Hi Gunjan
>
> just run recon-all and it will do everything
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 oth
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" wrote:
> Gunjan, this may be related
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 libtif
Hi Gunjan
if you are using bash, you need to run the instructions for bash at:
http://freesurfer.net/fswiki/SetupConfiguration
for example, it says:
If using bash or sh, type:
export FREESURFER_HOME=/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
cheers
Bruce
On
Tue,
18 Nov 2014, G
I followed the installation process from
http://freesurfer.net/fswiki/LinuxInstall.
while running "setenv FREESURFER_HOME /usr/local/freesurfer" it shows that
setenv command not found.
Is it necessary to place FreeSurfer directory in to /usr/local ? I have it
on my desktop.
On Tue, Nov 18, 2014
I think if the file existed you would have gotten a syntax error. Does it
exist? If not, then either you didn't install FreeSurfer there or something
went wrong with your installation
cheers
Bruce
On Tue, 18 Nov 2014, Gunjan Gautam wrote:
I ran but its showing error like below:
bibl04@BIBL0
I ran but its showing error like below:
bibl04@BIBL04:~/Desktop/freesurfer$ 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
wrot
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 /SetUpFreeSurfer.csh
before trying to run anything
cheers
Bruce
On Tue, 18 Nov 2014, Gunjan Gautam wrote:
H
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 obj
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
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
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
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" wrote:
> Hi Gunjan
>
> do you have a license? If not you need to download and install it (as
> noted in the error message). They
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 accord
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
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