Hi Tenny
That's troubling! What does it give you if you run it with a -v switch?
Is the SUBJECTS_DIR correct? It's one directory above 01_bay6/ and
02_bay6/ directories..
-Krish
On Dec 7, 2011, at 3:10 PM, te...@nmr.mgh.harvard.edu wrote:
> Hi All,
>
> I apologize if this is a simple fix, I
Hi Yuan
Can you find mris_calc in your $FREESURFER_HOME/bin/ ?
ls -al $FREESURFER_HOME/bin/mris_calc
Krish
On Sep 18, 2008, at 3:56 PM, Yuan Xu wrote:
Hi all,
Recently, I am doing command one by one on FreeSurfer Tutorial:
Process Flow. I got problem on command mris_calc as following:
Yuan,
I believe the best bet would be to install the latest 4.0.5 version.
Get it here - http://surfer.nmr.mgh.harvard.edu/fswiki/Download
We can put the latest mris_calc on our ftp if that's the only binary
you need.. but you might be missing other binaries. So once you
download 4.0.5 ple
Hi Jared
Could you give the script as well as the command you used to invoke
tkmedit?
Krish
On Sep 19, 2008, at 8:32 AM, Jared Price wrote:
Hi everyone,
I have written a simple script to automate the switching between the
grayscale MRI image and the segmentation volume. All it is is a
s information by persons or entities
other than the intended recipient is prohibited. If you received
this information in error, please contact the Compliance Help Line
at 800-856-1983 and properly dispose of this information.
Krish Subramaniam wrote:
Hi Jared
Could you give the script
Hello Kellen
Can you create a directory named tmp/ inside your subjects directory.
Suppose you had a subject named 'kellen'
cd $SUBJECTS_DIR
cd kellen/
mkdir tmp
and try again ?
If 'tmp/' already exists, make sure it's write-able.
Krish
On Oct 9, 2008, at 4:37 PM, Kellen Mobilia wrote:
Can you give me your platform? I'll see if I can put it online.
-Krish
On Nov 6, 2008, at 12:05 AM, Dominic Dwyer wrote:
Hi all,
Where I can find a copy of the mri_binarize file?
It doesn’t seem to be included with 4.0.5, and based on a post from
2007 I looked in ftp://surfer.nmr.mgh.harva
A command 'mri_convert' can do that
See http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
for a detailed description of the binary
Best
Krish
On Nov 17, 2008, at 5:57 PM, Al-Radaideh Ali wrote:
Dear FreeSurfer expert,
Any way that I can convert the mgz back to any analyze format so
tha
Hi Moe
Could you send us the data ( sig.nii .. directly to my email if it's
not big enough ). What steps do you take so that I can mimic the crash
here?
Thanks
Krish
On Nov 25, 2008, at 3:01 PM, Zeidan, Mohamed A. wrote:
Hi Everyone,
I'm trying to create a label but as I'm highlighting
Hi all,
For those who registered to our Freesurfer course (Jan 20,21 - 2009)
*on* or *after* Dec 18th, 2008.. due to a bug in our registration
page, we don't have your registration information in our database. We
request you to please re-register using that page again
http://surfer.nmr.mg
Hi Moe
Could you copy the output of the command "bugr" which ships with
Freesurfer. Just type bugr and send us. Basically, the exact workflow
so that we can recreate the problem here. Is it specific to that
particular volume?
Krish
On Jan 6, 2009, at 5:48 PM, Zeidan, Mohamed A. wrote:
Hi Alexa
One way is to use mris_volume to get that indirectly.
grey matter volume = pial volume - white matter volume.
Krish
On Jan 18, 2009, at 7:02 PM, Alexa Nardelli wrote:
Hi,
I was curious as to whether or not freesurfer obtains a total grey
matter volume?
Thanks
Alexa
___
Hi Jennifer
When did you download the data? We overhauled the tutorials and I
believe Nick updated the wiki with the new data couple of days back.
Please download the new one and try.
Krish
On Jan 21, 2009, at 3:56 PM, jbr...@ucla.edu wrote:
Hello -
I am a new graduate student working w
We have done a rewrite of both aparcstats2table and asegstats2table,
although it needs a little a bit of testing, still. I'll put the new
version online and send you the link soon. It will be great if you can
test i) the bug in question and ii) aparcstats2table in general.
Both will definit
Hi Diana
I've put it here.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/stats2table_alpha.tar.gz
To install
cp stats2table_alpha.tar.gz $FREESURFER_HOME/bin/
cd $FREESURFER_HOME/bin
tar zvxf stats2table_alpha.tar.gz
The binary is named "aparcstats2table_re" ( _re for rewrite
Hi Diana
I have put the latest rewrite ( more fixes and updates ) of both the
aparcstats2table and asegstats2table here. If you still haven't tried
with the previous one we sent you, use this version instead.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/stats2table.tar.gz
Ext
Hi Diana
Sorry. For a quick fix, could you open up aparcstats2table, go to line
# 108 where it says
choices=('aparc', 'aparc.a2005s'),
and delete that line.
Make sure the indentation of the next line is not disturbed
and it should work.
Krish
On Feb 6, 2009, at 5:30 AM, Diana Wotruba wrot
Hi Jürgen
The default behavior of the rewritten aparcstats2table is it takes the
UNION of all the parcellations and writes them to a table. For instance
Suppose subject sub1 has parcellations parc1 and parc2 and
subject sub2 has parcellations parc2 and parc3
the union of parcellations is parc
made a UNION across several subject
numbers (different single subjects, 10, 50, 104)?
Thanks for clarification
Regards
Jürgen
On 7.2.2009 18:33 Uhr, "Krish Subramaniam"
wrote:
Hi Jürgen
The default behavior of the rewritten aparcstats2table is it takes
the
UNION of all the parc
Hi Pål
Check this thread out
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07545.html
anyway did you do anything to your system which might have overwritten
your Nvidia drivers? Re-install the latest drivers for your graphics
hardware and try again.
Krish
On Mar 9, 2009,
And just a note that aparcstats2table ( as well as asegstats2table )
has been revamped.
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes See under "Known
Issues" on how to get the new version
Re: Mike's command line.. the new version will complain about "--h"
option since there are two
Hi giovanni
Could you try with
setenv doublebufferflag 1
and then run tksurfer again?
On Mar 20, 2009, at 1:13 PM, Battistella Giovanni wrote:
Dear freesurfer users,
I've just installed freesurfer on my PC and I tried testing it using
the sample subject.
tkmedit works fine, but with tksurf
Hi Anita
Apologies. fsutils is one of the 4 helper scripts that I forgot to put
in the distribution.
Please get the 4 scripts from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/datastruct_utils.py
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/fsutils.py
ftp://s
Hi Tori
the --statsfile option is now --stats i.e use --stats name> That in conjuction with --subdir will work.
I'll update the documentation ( which still says --statsfile and is
wrong... sorry! )let me know how it goes.
Thanks
Krish
On Apr 8, 2009, at 10:36 AM, Victoria Williams wrote:
lease.
Thanks
Krish
On Apr 8, 2009, at 2:40 PM, Krish Subramaniam wrote:
the --statsfile option is now --stats i.e use --stats name> That in conjuction with --subdir will work.
I'll update the documentation ( which still says --statsfile and is
wrong... sorry! )let me kno
If you mean save the screenshot to an image without the background
( the background is transparent), you can do so with the free GIMP.
The tool is in one of the menus and it's called "Select by Color",
click the black portion and cut it.
Save it to an image format which understands transpar
Hi Falk
fsutils is one of the 4 helper scripts missing from the distribution.
Please get the 4 scripts from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/datastruct_utils.py
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/fsutils.py
ftp://surfer.nmr.mgh.harvard.edu/
One more comment
if you are looking to run recon-all after that, that 001.mgz should be
inside orig/
cd $SUBJECTS_DIR/mri/orig
mri_convert 001088.dcm 001.mgz
should work I guess.
Even that step is not needed in the case of recon-all, see
http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFree
We have managed to get an experimental build of mac working but it's
very unstable. We'll include in the distribution if we see improvement
in the stability with respect to VTK and wxWidgets Mac libraries ( and
their interoperability ) which freeview depends on. However, it runs
nicely on C
We also publish md5 checksums for the large downloads we have at the
site. These are quick-fire way to check whether the (huge) file you
downloaded is intact. The binary "md5sum" should be there in almost
any Linux distribution. Just give this command to the file you've
downloaded
md5sum
Yes, type 3 is an MGH/MGZ file.
On Jul 11, 2009, at 1:42 PM, Bruce Fischl wrote:
Hi Lars,
can you send us the whole command line and output? I think type 3 is
an MGH/MGZ file. Does mri_info work on it properly?
cheers
Bruce
On Sat, 11 Jul 2009, Lars M. Rimol wrote:
Hi,
What does it me
Hi Rosa
Sorry, this was a bug related to the table producing scripts in a
previous version of FreeSurfer which was fixed subsequently. Get the
files from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/asegaparcutils/datastruct_utils.py
ftp://surfer.nmr.mgh.harvard.edu/transf
Hi
On Ubuntu, you will need to do the following:
cd /usr/lib
sudo ln -s libtiff.so.4 libtiff.so.3
( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download )
The second command only works if you have write access to /usr/lib..
otherwise you could contact your sysadmin.
Krish
On Jul 24, 2009, a
How can I solve the problem... How
> can I
> specify to freesurfer that the lib is in another folder ?... Any
> idea ?...
>
> SIncerely,
>
>
> Gonzalo Rojas Costa
>
>
> Krish Subramaniam escribió:
>> Hi
>>
>> On Ubuntu, you will need to do the f
Hi Sharmili
Can you copy and paste the text which tksurfer shows when you try to
open the label? You have attached an image and it doesn't seem to show
the entire text.
Krish
On Jul 27, 2009, at 6:54 PM, Sharmili 57 wrote:
> <20090727-171126.png>
___
What if you rename the file liwentao_1.mgz to liwentao_1.mgh.gz
mv liwentao_1.mgz liwentao_1.mgh.gz
and gunzip it
gunzip liwentao_1.mgh.gz
this should work. If this doesn't work, it means the file is corrupted.
If it works, use the resulting file "liwentao_1.mgh" as an input to
recon-all
>>
Hi Jon
Get both the files from /space/outgoing/fsdev/krish/freeview/
copy them to $FREESURFER_HOME/bin/ and
tar zvxf freeview.tar.gz
and make sure $FREESURFER_HOME is set
setenv $FREESURFER_HOME
then execute freeview.nmr.sh
./freeview.nmr.sh
I haven't had the time to check it in any mac. B
Yes, everything Rudolph said.
Also, the FreeSurfer we package for Ubuntu is actually a CentOS build
because Ubuntu is a flavor of linux like CentOS and since FreeSurfer
package is self-contained everything should work once you un-tar-gz.
The only things we don't bundle are X server and OpenGL
- Do they have proper permissions?
ls -al $FREESURFER_HOME/bin/*stats2table
-if they do.. might something be wrong with the default Python?
can you paste the entire output you get?
Krish
On Oct 26, 2009, at 12:29 PM, Andrew Jahn wrote:
> Hi,
>
> I am running FreeSurfer version 4.3, and when I
am using Python 2.4.4. Does FreeSurfer require a different version?
>
> Thanks,
>
> -Andrew
>
>
> On Mon, Oct 26, 2009 at 12:36 PM, Krish Subramaniam
> > wrote:
>
> - Do they have proper permissions?
> ls -al $FREESURFER_HOME/bin/*stats2table
>
> -if they
Some programs notoriously add Ctrl-M at the end of every line ( or
every cell )
If you have the vi editor you can follow this method
http://www.tech-recipes.com/rx/150/remove-m-characters-at-end-of-lines-in-vi/
to remove all the instances of Ctrl-M and again try in qdec.
Unfortunately I am
Hi Ilana
The double slashes shouldn't matter. What does it say when you give
tkmedit bert brainmask.mgz
in the freesurfer environment ( i.e. after you run SetUpFreeSurfer.csh )
Krish
On 12/14/09 5:27 PM, Ilana Hairston wrote:
> Hi there,
> I moved my data to a new computer with Freesurfer inst
Please find the download information in the following wiki-page --
http://surfer.nmr.mgh.harvard.edu/fswiki/Colin27
Thanks
Krish
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The following mis-feature highlighted by Nathan is fixed and the fixes
are available from the following location. Replacing your existing
aseg/aparcstats2table is highly recommended.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/
Please copy the files to your $FREESURFE
Hi Ed,
What do you exactly mean? The right click and drag doesn't remove the
voxels and the middle click and drag doesn't add the voxels? I tried
it and it works for me.
I've copied the nightly build to
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/intel-mac/tkmedit.bin
Hi Ali
I've enabled a command in the latest dev build which does the
following. This only prints the vertex without any other details.
% print_nearest_vertex_to_talairach_point -53.34 -7.81 -4.5
surfer: vertex 86131
Let me know your platform by an email off the list ( type freesurfer
when yo
Hi Amir
1. Try and check if the file you downloaded has the md5 checksum
listed here -- http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/md5sum.txt
For the Suse Itanium one, the string of characters you are looking for
is "e064d9a8b08dc10ecc57d1b60f0094f"
To find out the md5, use the co
Hi Tyler
qdec makes use of bunch of scripts. In this case, when you analyze it
makes use of "asegstats2table". To know more about it type
asegstats2table --help
in your environment. The error is: one of the aseg.stats is has
different number of segmentations than all other ( or there is a go
Here you go Yaroslav...
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
Krish
On Apr 24, 2008, at 11:49 AM, Yaroslav Halchenko wrote:
actually I need thickness data out of it. Is .mgh format documented
somewhere?
On Thu, 24 Apr 2008, Pádraig Kitterick wrote:
How much detail d
Hi Yaroslav and Pádraig,
Please follow the link pasted below to get an alpha version of pymgh.
It requires the latest Python and Numpy.
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/10224/1/2a5da2a125134fbdfc9e6850be1fcc09
(expires in 30 days )
Make sure PYTHONPATH has the d
Navaneethan,
To answer #2, .mgz is indeed gzipped .mgh but gunzip probably doesn't
recognize the suffix.
cp foo.mgz foo.mgh.gz
gunzip foo.mgh.gz
should work.
-Krish
On May 19, 2008, at 3:46 PM, Navaneethan Santhanam wrote:
Hi Freesurfer gurus & experts,
I'm trying to port Freesurfer data
Others ( Paul, Nick) might chip in with a much better answer but my
guess is your problem might be related to this thread earlier on the
list..
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07324.html
--Krish
On May 27, 2008, at 11:30 AM, Juranek, Jenifer wrote:
Hi,
I recen
Liat,
Could you tell us the browser you are using? Because we have been
using the fswiki without problems. ( and I can access fswiki from my
home, hence we can rule out the case that fswiki is not available
external to our center )
https://surfer.nmr.mgh.harvard.edu/fswiki
and
http://su
Marlisa,
The memory ( RAM) you have? My guess is if Freesurfer uses significant
amount of swap, it becomes slow. Is it different from other 2 machines
or the same order of magnitude?
If time permits, could you send the "Hardware Overview" information?
( Apple Icon in menubar->About this M
Aaron and Bruce,
Looks like tkmedit saves edit.dat in the directory from which it is
invoked, but tksurfer tries to load edit.dat from the tmp/edit.dat in
the subject dir.
A simple workaround is to setenv a variable called FS_SAVE_GOTO_POINT
to a filename where you want both tkmedit and t
Hi Narly
You should install the Leopard version if you have 10.5. Here's the
download page
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
We need to update the Installation wiki page because we also support
Leopard now.
-Krish
On Jun 20, 2008, at 7:47 AM, Narly A Golestani wrote:
Hi Eliezer
We changed the search system couple of months back but sometimes the
search takes a bit of time, yes. Could you give me an example query
you gave, the page you expected and what the search results turned out
to be?
Also, use the "Text" search function rather than Title search bec
Hi Maria
The SUBJECTS_DIR is one directory above the my_subj_name. Sorry if
this is a trivial point, but worth a check.
can you give me the output of following commands
echo $SUBJECTS_DIR
ls $SUBJECTS_DIR
On May 12, 2010, at 7:03 PM, iac...@nmr.mgh.harvard.edu wrote:
> Hi all!
> I have some
FYI..
Begin forwarded message:
> From: iac...@nmr.mgh.harvard.edu
> Date: May 13, 2010 3:11:09 PM EDT
> To: "Krish Subramaniam"
> Subject: Re: [Freesurfer] problems with tksurfer
>
> Thanks Krish!
> you solved my problem.
> I mean, I made just a small error
Hi Lena
Do you have a Mac? In that case, I can send you an experimental build
of freeview if your OS is 10.5.x ( Leopard ). It doesn't work on
10.6.x ( Snow Leopard ) which we are working on.
Best
Krish
On May 19, 2010, at 3:37 PM, Bruce Fischl wrote:
> it should be in our current distribut
Hi Jesse
Can you do
gzip -d fsfast-tutorial.tar.gz
and then do
tar -xf fsfast-tutorial.tar
If this works, I am guessing it might be an error of the command "tar"
itself ( how it's implemented across platforms )
Best
Krish
On May 25, 2010, at 1:37 PM, Jesse Friedman wrote:
> Thanks... I di
Hi Jason
Try this under tcsh
setenv double_buffer_flag 1
it is known to work for certain platform/freesurfer combos
Krish
On Jun 1, 2010, at 9:15 PM, Bruce Fischl wrote:
> Hi Jason,
>
> have you tried updating the video driver? I think that's the standard
> solution. Nick is traveling so won'
Hi Seok
Can you send us the mri volume and I'll take a look.
Krish
On Jun 10, 2010, at 5:29 PM, Seok Lew wrote:
> Hi,
>
> I am using matlab functions of MRIread and MRIwrite for a MRI
> correction. When running mri_normalize with the corrected MRI, I came
> up with the error like 'unsupported
Hi Gaelle
This seems to be an error due to Python's "warning" module being
deprecated in Python 2.6. I'll update the sources so as to accommodate
this change.
Meanwhile, the quickest fix is to open up
nano $FREESURFER_HOME/bin/asegstats2table
and comment out the following lines ( put a "#"
Hi Sebastian
I was able to manipulate the dialogue like this
%set gEditBrush(1,cloneSource) 1
%set gEditBrush(1,mode) 1
Try a combination of 0 or 1 for the last argument. And spaces ( or
lack of them ) are absolutely important. Don't leave any space in
gEditBrush(1,mode)
The first argument
Hi Serena
It means you don't have write permissions in the directory. You should
invoke pico like
sudo pico /Applications/freesurfer/.license
..it'll ask for your password and save successfully, provided you have
permissions.
-Krish
On Aug 1, 2010, at 8:32 AM, sere f wrote:
>
>
> Hi All,
Hi Corinna
I think most likely it's the division operator ( / ) you used in the
line
gwratio.vol = gray.vol/white.vol;
Element-wise division in MATLAB is achieved by a ./ . I think the line
should be
gwratio.vol = gray.vol./white.vol
You could debug it by placing a
size(gwratio.vol)
imme
On Sep 2, 2010, at 2:49 PM, corinna bauer wrote:
> Thank you, that seems to have done the trick.
>
> On Thu, Sep 2, 2010 at 2:13 PM, Krish Subramaniam > wrote:
> Hi Corinna
>
> I think most likely it's the division operator ( / ) you used in the
> line
>
>
Hi Rafa
Might be because MATLAB uses 1-based indexing?
What if you compare the values of the PET in tksurfer and
vol(numberOfVertex + 1) ?
Best
Krish
On Sep 3, 2010, at 10:17 AM, Rafa x wrote:
> Dear Freesurfers,
> I’m trying to obtain in matlab the PET value of each vertex of the
> cortex f
Hi Adam
Is this for the FreeSurfer 5.0.0 virtual machine? The password is
"freesurfer" ( without the quotes ).
Cheers
Krish
On 10/11/10 4:43 PM, Eggebrecht, Adam wrote:
> The README file explains how to gain access to a USB device, not how to
> internally mount the shared folder.
> The only wa
__
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Krish Subramaniam
> [kr...@nmr.mgh.harvard.edu]
> Sent: Monday, October 11, 2010 4:12 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] password for windows ubuntu
:58:37 -0500
From: Eggebrecht, Adam
To: Krish Subramaniam
Ah, excellent.
Thank you, Krish!
-Adam
Adam T. Eggebrecht, Ph.D.
Dept. of Radiology
Washington University School of Medicine
St. Louis, MO
314-362-6942
From: Krish Subramaniam [kr
Hi Jesse
It seems there's something wrong with your Python installation.
Can you do the following?
type
python
and in the interpreter, enter
import os
and see if it works.
-Krish
On Dec 4, 2010, at 6:48 PM, Jesse Bledsoe wrote:
> Hello FreeSurfer group,
>
> I am unable to run asegstats2ta
No module named os
> >>>
>
> Any suggestions?
>
> Jesse
>
> On Mon, Dec 6, 2010 at 2:12 PM, Krish Subramaniam > wrote:
> Hi Jesse
>
> It seems there's something wrong with your Python installation.
>
> Can you do the following?
>
> type
>
&
Hi Catherine
You need to mount the external harddisk inside the
virtualbox and give its path as $SUBJECTS_DIR.
The path starting with E:\data\.. is how Windows 7 sees the harddisk.
Unfortunately, there is no easy way to do this.
* The hardwork is to make the Guest OS ( ubuntu in this case ) s
Hi Krista
If the directory tree is something like
$SUBJECTS_DIR
|
| P01
| |-- stats
| || lh.G_cuneus.stats
| P02
| |-- stats
| || lh.G_cuneus.stats
where P0? are the participants subjects directories.. U
Sorry, this is a known bug. I'll send an email once it's fixed
Best
Krish
On May 23, 2011, at 3:21 PM, Gonzalo Rojas Costa wrote:
> Hi:
>
>I have an ubuntu based computer with Freesurfer 5.0.0, and the
> lowest part of the View->Configure->Overlay window of tksurfer
> didn't appears (see
Hi Hyunwoo
Our build system seems to pick up the dynamic gfortran libraries for
OSX. We'll post a fixed mri_robust_register ( and similar binaries
which depend on that dynamic library) soon.
For a temporary fix:
save
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/libgfortran
Hi,
And Mac users should wait for this instead of my suggested temporary
fix earlier today.
Thanks,
-Krish
On May 25, 2011, at 2:57 PM, Nick Schmansky wrote:
> Hyunwoo (and Mac users),
>
> We're going to have to post a new build of v5.1 later today which
> fixes
> this problem. In general,
Hi all,
It's been pointed out that tksurfer's "Configure Overlay Display"
dialog gets clipped for low resolution monitors where it's impossible
to see and interact with the buttons. This is how it looks:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurferclipped.jp
Hi Ashley
Can you tell us in detail what OS you have? ( The version number ).
Also, what commands specifically were you trying to run?
Thanks
Krish
On Tue, May 31, 2011 at 11:45:39AM -0400, an...@pitt.edu wrote:
> Hi,
>
> I recently downloaded and installed FreeSurfer on my Mac and I am having
Hi Mike
Sorry. Our OSX builds seem to pick up the dynamic libraries for a few
binaries during the build process. These things escape our internal
testing because the binaries work here.
We'll post a new build which takes care of this issue. This can be
just installed over the existing 5.1 v
dit.bin in tktools dir
The installation needs to copy these files to both the locations and we
think that it didn't do it somehow.
-Krish
On Tue, Jun 07, 2011 at 01:32:56PM -0400, Krish Subramaniam wrote:
> Hi Mike
>
> Sorry. Our OSX builds seem to pick up the dynamic libraries for a
Hi Daniel
You get permission denied because you need write permissions for /usr/
lib ( wherever libtiff.so.3 is ).
If you think you have the permissions, prefix your "ln" command with a
"sudo" and it'll ask for your password, and that should work
successfully.
If you don't have permissions,
Hi Lin
When you extracted the archive, did you encounter any errors? You seem
to be following the right steps.
Also check if the md5 sum is correct
$md5sum freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz
It should output ba9d374e611d7a22a4c484e333b60b4c
(see http://surfer.nmr.mgh.har
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