Recently Microsoft announced bash on Windows and initial tests within our
group have shown that freesurfer and freeview work in this environment:
https://msdn.microsoft.com/en-us/commandline/wsl/about
However, currently freeview is not shipped as a separate stand-alone
package from freesurfer.
Thats odd. Does that file exist? What are the permissions of it?
ls -l
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz
> IPL Neurosurgery has shared aâ¯OneDriveâ¯file with you. To view it,
> click the link below.
>
>
>
Usually it would be /usr/local/freesurfer
If thats what you did than you may need root access to the machine to be
able to do that. So basically create the license.txt file in your home
directory than copy it to the frresurfer folder:
sudo cp license.txt /usr/local/freesurfer/
Bottom line is
Hello Daniela,
Ive been looking into this error, and although I am unable to replicate it
on my Mac, I do have what might be a potential solution. Could you please
source freesurfer, then run the following command.
$> sudo -E fs_update
Then retry the subject with the parallel flag. Please let
Hello Fred,
Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of
curiosity, did freesurfer 5.3 exist on your system before installed 6.0?
That error shouldnt happen if FS6 is cleanly installed and definitely
shouldnt happen of SIPS is disabled.
I suppose as a last resort
Hello Francis,
Yes, Richard is correct. When doing a local installation you will need the
freesurfer data files which do not come with a default clone of the repo.
Please see section 1.1 of the build page:
$>
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
To get
I just did a test download on my home network and I got the correct sha
1723ef916c4e74ee8fff72438e9c6c91c79bd4cb
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
Perhaps your network times out after a certain time period, or has a cap
on the file size?
> sha1sum
This error is due to an incompatibility between the version of perl
shipped with ubuntu16 and the MINC tools shipped with freesurfer. This
issue has been fixed in freesurfer version 6.0, which I recommend you
download and install.
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
If your question is whether you can install multiple versions of
freesurfer on your linux workstation, than the answer is yes. Just be sure
they are located in separate directories and be sure to set your
FREESURFER_HOME environment variable correctly.
-Zeke
> Dear FreeSurfer experts
>
> I
Hello Juhyoung,
If its complaining about "RB_all_2008-03-26.gca" then something must have
happened where you still have portions of the old freesurfer installed, or
your mixing versions because Freesurfer v6 has no mention of
RB_all_2008-03-26.gca. Please try completely removing the
The new version wont work in the FS5.3 framework. Its needs to be packaged
within the development version for it to work.
Whats the error? And does it only happen with one subject data, or all
subjects?
> Hi list,
> mri_mcsim on FS5.3 is giving a strange error in osx 10.11, in the wiki a
> newer
To get 5.3 working on machines with perl 5.22 or later I will refer you to
the following thread:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50383.html
I cant say for sure how many mni scripts will need to point the the older
version of perl, its probably subjects
The dev version of freesurfer (and the upcoming v6 release) is compatible
with Centos7 and also fixes the perl/MNI issue.
> Hi!
> I was wondering whether there is an update from the 2014 thread on
> Freesurfer's compatibility with Centos 7? The old thread is here:
>
Hello Peter,
I understand your dilemma, its unfortunate the updated version of perl
causes the MNI tools to fail. If you MUST use freesurfer 5.3 on an Ubuntu
16 machine there is only one way that I can think of to make it work:
You need to install perlbrew and use that to install perl version
We will be momentarily releasing a beta version of freesurfer version 6
that solves this issue. You can download and install that version which
will work on your opensuse 13.2 platform.
Otherwise you will need access to an older version of the libcrypt file
from opensuse 12.1 (which I dont have
This page should be more helpful for you.
http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
-Zeke
> I am trying to checkout the development version of Freesurfer from the CVS
> repository. I need to build against VTK 7.1 instead of 5.6 for freeview
> and am using
> Hi
>
> I am using recon-all in some longitudinal data on a ubuntu 16.04, and
> using
> the development version of freesurfer as I was told here, because the
> other
> current version doesnt work on ubuntu 16.04.
>
> The problem is that the first scans were probablly processed using
>
The FreeSurfer Software License Agreement does not contain any language
explicitly or implicitly preventing commercial usage, however I will
highlight the following text from the License Agreement:
"Any commercialization of the Software is at the sole risk
of the party or parties engaged in
Hello Paul,
Doug is essential correct. You can download 5.3 (or the development
version) and just extract it to a different location. Something like:
$> mkdir /usr/local/freesurfer_5.3
$> tar -C /usr/local/freesurfer_5.3 -xzvf
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Then
Hello Lee,
Opensuse platforms versions greater than 12.1 are not compatible with the
FreeSurfer licensing scheme, but their are workarounds. I will contact you
offline so we can figure out the best solution for your setup.
-Zeke
> Hi,
> Our IT department have recently upgraded our cluster OS
Hello Fred,
Yes, newer development binaries on Mac are not compatible with previous
releases of freesurfer. If you wish the use a newer binary you will need
to use the latest developmemnt version of freesurfer. This can be
downloaded from the following page (see "Development Version"):
Current versions of the Mac freesurfer binaries are not compatible with
the v5.3 release. Too much has changed since then. If you wanted to use
the newest version on the code you will need to download the latest dev
version of freesurfer from this page (see "Development Version"):
Yes this is a good idea. All subsequent 3rd party bundles will be
versioned as (or similar to) the way you describe below. Which is good
because a new one will be released soon. Thanks for the input.
-Zeke
> ATM
>
Intolerable differences have not been found. They are always minor <%5 and
their source can come from several places. For example, different
compilers (or even different versions of the same compiler) can have
different sorting behavior when presented with objects that have
equivalent comparators.
This topic gets brought up occasionally and their are valid arguments to
both sides. One reason we have hesitated to use dynamic libs is the partly
due to freesurfers long release cycle (all subjects that are part of a
study need to be performed all on the same version). This long release
cycle
You need to provide input data for the subject. This would either go in
the 150622fracal/mri/orig folder or use the -i flag to point to the input
file.
-Zeke
> After this command
> recon-all -all -s 150622fracal -hippocampal-subfields-T1
>
> this error come out:
>
>
>From the recon-all wiki page under "specify input":
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Specifyinput
In this case you would use the -i flag to point to dicom file or nifti.
For example:
recon-all -all -s 150622fracal -i
-hippocampal-subfields-T1
-Zeke
> Hi Zeke,
> I'm
Hello Emad,
Thank you for reporting this. Its a bug specific to the latest version
of OS X (El Capitan). I have committed the fix and it will available
after the nightly build. You can download via this link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
Sorry for the
Did you source the Freesurfer setup script?
$> export FREESURFER_HOME=/Applications/freesurfer6
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh
> Hello All,
>
> I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am
> getting the following error when I run recon-all from
Hello Neda,
Hello Neda,
Can you please send me an email with a copy of your .license file as an
attachment? *Please send it to my direct email address* and not to the
Freesurfer support list. I will take a look and send you a valid license
file if necessary.
-Zeke
> Hi Bruce,
>
> I'm sure
There were some recent changes in the build that eliminated the necessity
for that library. Casper, can you try using this most recent version and
let me know if it works?
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg
Thanks,
-Zeke
> Zeke, is
Oh, Sorry about that, I was unaware you were using freesurfer v5.1 on an
older RedHat system.
Freesurfer v5.1 was released quite awhile ago and its entirely possible
that the newest development version of the freesurfer binaries are not
compatible with it. But here is a link to our centos4 build
This is an unfortunate consequence of mixing and matching various
subcomponents of freesurfer. I will private message you a potential work
around.
-Zeke
> Dear FS experts
>
> we are running TRACULA on a Mac (OS X 10.7.5) and faced an error related
> to mri_convert.
>
> we then donloaded (as
My guess is that you are using Safari on a Mac OSX Machine? If so, I have
observed that Safari has strange behavior with ftp links. Can you try
using another browser like Firefox or Chrome? Or, you can download by
typing the following command in a terminal window:
$> curl -O
Is is a warning or an error?
Passing the --disable-Werror flag to the configure script will prevent the
build from erroring out if it comes across a warning from the compiler. I
havent testing on Ubuntu 15 but I will give it a shot early early next
week.
-Zeke
> I'm preparing to migrate over to
Hello,
This is a known when running freesurfer on Ubuntu systems. The solution is
addressed in the FAQ section on the frresurfer download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
pecifically, the solution is to go into you system's lib directory and
create a symlink as
Ah, I see. This issue must have arisen due to some changes I made in the
freesurfer git repository.
Eugenio, I should have this resolved by tomorrows build.
Alexandra, thanks for pointing this out. It should be fixed in tomorrows
daily build. Ill send you an email to confirm.
-Zeke
Hi Zeke
Hello Caspar,
I did a quick test and it appears the new dev version of mri_label2label
is still compatible with the version of 5.1 that you have. Please use the
following link to download it and also please make sure to back up the
version you already have.
As the error message indicates, this is a permissions issue. To solve the
license problem, your best bet is to create the license files in your home
directory (or anywhere you have adequate permissions) and copy it to
/Applications/freesurfer. This is described in a little more detail in the
Hello,
Here is a download link to the most recent version of mri_tessellate:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_tessellate
Please place the new version in your $FREESURFER_HOME/bin directory, and
backup the original. Hope this helps.
-Zeke
I would be very interested on the data set (and exact command) you used
that exhibited a 25% speed up. Because our tests showed little to no
improvement in run time when using the -march=core-avx2 during compiling.
-Zeke
Oh PS, AVX gives about 25% speed up compared to SSE. Would it be useful
Hello Feng Liu,
What is the terminal output when you enter the following commands:
$ cd /media/sf_E_DRIVE/output/nv001/mri
$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i orig.mgz --o orig_nu.mgz
-Zeke
Dear freesurfer experts,
I came across a problem when I run
Have you verified that the machine you are ssh'ing into will display
tkmedit even if you are not ssh'ing into it? I ask because OSX 10.6 is an
end-of-life operating system and that error is usually associated with
incompatible graphics card.
However, even if it did work while sitting at the host
Hello,
Is there any detailed information on the possible differences in results
wwhen upgrading to the latest FreeSurfer software?
As it pertains to the scans already processed with old software compared
to
any scans processed with a newer version of the software.
When freesurfer6.0 is
Hello Isabelle,
Freeview has been undergoing many changes and you simply got unlucky and
downloaded an unstable version of the program. I will be posting an
updated version within the day and I will email you directly when it
becomes available.
-Zeke
htmlheadmeta http-equiv=Content-Type
Can you please provide me with the Processor and Graphics hardware
specs of the machine listed under Apple - About This Mac.
Ive only ever seen this error on old mac minis and its usually indicative
of an incompatible graphics card.
Dear freesurfer,
I tried using kvlThresholdImage on a MacOSX
I'm testing the total processing time of recon-all -all using -openmp
4,6,8,12 .
The runs with 4 and 6 threads took almost the same amount of time.
The runs with 8 and 12 threads took almost the same amount of time.
(1)Is the work divided evenly between the threads (mri_ca_register,
A-reum,
Opening jpeg compressed dicoms is new feature so please bear with us as we
try and get this working for you. Use the link below to download the
libdcmjpeg.so.3.6.0 file.
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/libdcmjpeg.so.3.6
Once the download
A-reum,
Please download the following file:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/dcmdjpeg.fs
And replace your existing $FREESURFER_HOME/bin/dcmdjpeg.fs file with the
one from the link above. Also, make sure it is set to executable by typing
the
Hello Emad,
The download page states that OSX versions of freesurfer require the user
to download and install XQuartz onto their machine. I have updated the
download page so it is a little more clear.
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Also, the dev version of freesurfer is in a
The freesurfer installation does NOT contain a license file. You must
create it, first by creating a file called license.txt in your
FREESURFER_HOME directory, then copy/paste the contents specified in the
email you recieved into the license.txt file.
-Zeke
Hi,
I downloaded the latest
The 64bit Lion version. It should probably be made a little more clear
that that version is for 10.7 and higher. Ill fix that.
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
-Zeke
Gentleman
Which Version of Freesurfer should I download for use with the OS X
Yosemite 10.10.1?
Thanks
Yes, please try running as root and get back when you have the chance.
This is a very odd issue and your results when running as root will
provide insight.
-Zeke
Hi Z K,
Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one
installed with the latest freesurfer version
Hello Alessandra,
This is a known issue with pre-freesurfer v5.3 releases and the most
recent version of Ubuntu. To fix the issue, if you have access to a
machine that still runs Ubuntu 12.04, please do the following:
1) On the Ubuntu 12.04 system, find the find the file libcrypt-2.*.so
Bruce,
By symlink from your /mnt/hgfs/mydata/fsaverage to
/usr/local/freesurfer/subjects/fsaverage you mean ln -s
/mnt/hgfs/mydata/fsaverage /usr/local/freesurfer/subjects/fsaverage ?
which fsaverage is the target ?
Thanks,
Mahmoud
The target fsaverage is the one that came with the
Here is the proper link.
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/fsaverage.tar.gz
Bruce,
By symlink from your /mnt/hgfs/mydata/fsaverage to
/usr/local/freesurfer/subjects/fsaverage you mean ln -s
/mnt/hgfs/mydata/fsaverage
Mahmoud,
If I recall correctly, your on a virtual machine with the /mnt/hgfs/mydata
directory being a shared directory, and you werent able to write to it
when running recon-all.
So, what you want to do is create another directory within your virtual
machine that holds your subjects data. You
I believe if you simply run:
$ recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject
case018_tp2 -all
You should be all set. You do not need to type any of the following commands:
clear
cd /volumetric
ln -s /usr/local/freesurfer/subjects/fsaverage
-Zeke
Zeke,
I created
Hello Rujing,
You can download the most up to date version of freeview using the
following link:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/
In order to use this version, you will need to replace the file
$FREESURFER_HOME/bin/freeview.bin currently on your system
to date version of freeview using the
following link:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/
In order to use this version, you will need to replace the file
$FREESURFER_HOME/bin/freeview.bin currently on your system, with the file
you download from the link above
Hello Sal,
I tried setting my display to :0.0 and was able to get the tkmedit program
to open on my Mac Mountain Lion machine so Im not exactly sure why yours
is having difficulty. Have you installed XQuartz?
http://xquartz.macosforge.org/landing/
If you already have XQuartz installed I would
Hello,
Is this running in Ubuntu? If so, it should be solved by running the
following command:
$ sudo apt-get install libjpeg62
-Zeke
Dear All,
When I tried to running qdec, I'm getting the following error.
qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
shared
Nate,
Try typing the following from the command window:
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
Or, you can add these lines to your .bashrc file in your home directory by
using any text editor, or by typing the following in the command line:
Mike,
I have tested the download from multiple computers on multiple different
networks, including my home network. It is successful everytime. I dont
know if you have a a system administrator who can help resolve the
situation on your end but everything seems to be running correctly on our
side.
Daniel, Stefano, Others,
A patch is now available for the mris_resample : Command not found
error you encountered.
Simply download the file from the following link and place it in your
$FREESURFER_HOME/bin directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
Flavia,
You are going to have to be a little more specific in describing what you
are trying to do and what exactly the problem is. You say you cannot open
the example Bert... What does that mean? You can open it in tkmedit? What
is the error?
The procedure for getting the license is to go to
Gari,
This is definitely an XQuartz issue. Have you rebooted your system since
installing XQuartz? Does /opt/X11/lib/libGLU.1.dylib exist? In my
experience, installing XQuartz can be a finicky process that sometimes
requires at least one reboot and a logout/login. If rebooting doesn't
solve your
Hello Nooshin,
The email containing the registration page went out today at 11am EST. It
can be found here:
https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.7678.cgi
Unfortunately, the course was filled within the first two hours of opening
registration, but there is a waitlist and
Hello Sudhin,
From what I can tell, it appears that is it possible you have a
compatibility issue between Exceed OpenGL and Mesa GLX (and thus not
directly a freesurfer issue).
It turns out if your system's libGL.so library is provided by Mesa
7.1 or later, OpenGL applications will not run
cc'ing the freesurfer list so other with the same issue may reference.
Original Message
Subject: Re: [Freesurfer] tkregister2 window error: Remote login
From:Sudhin A. Shah sut2...@med.cornell.edu
Date:Fri, February 22, 2013 10:51
Hello Kalli,
In the past this issue has been related to out-of-date NVIDIA drivers. If
you open a terminal and type 'glxgears' do you see a window pop-up
with 3 colored gears running? If not, email the help desk and ask them to
update your NVIDIA drivers.
-Zeke
Hi all,
I am a new student at
Hello Krista,
freesurfer v5.0 does not have a Lion build. Im fairly certain Lion did not
even exist when 5.0 was released. I suggest you give the Leopard build a
try, I *think* it will work, but I haven't tested it.
If you download the the .dmg file the install should be fairly self
explanatory.
I just noticed their are two Leopards builds... go with the leopard-i686
version.
-Zeke
Hello Krista,
freesurfer v5.0 does not have a Lion build. Im fairly certain Lion did not
even exist when 5.0 was released. I suggest you give the Leopard build a
try, I *think* it will work, but I
Hello Carl,
Some of the freesurfer GUIs require XQuartz. Unfortunately, XQuartz is no
longer installed by default on Mac 10.8. You can download and install
XQuartz from here:
http://xquartz.macosforge.org/landing/
-Zeke
Dear Freesurfer,
When trying to start qdec I get the following error:
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