On Sunday, December 02, 2012 23:56:38 Yaniv Kaufman wrote:
> Dear Freesurfer experts,
>
> I am trying to display DTI using freeview, however, every time I attempt to
> run freeview from the command line (I am using Ubuntu 12.4), I receive the
> following error:
>
> "freeview.bin: error whil
Dear Freesurfer experts,
I am trying to display DTI using freeview, however, every time I attempt to run
freeview from the command line (I am using Ubuntu 12.4), I receive the
following error:
"freeview.bin: error while loading shared libraries: libjpeg.so.62:
cannot open shared objec
Hi, Freeview does not look up SUBJECT environment variable. So you will
need to cd into your subject directory before running the command, or
use the full path in the command for every file.
Ruopeng
On 11/7/12 9:50 AM, Catherine Bois wrote:
Hi, I am trying to use freeview to look at wm/brainma
Hi, I am trying to use freeview to look at wm/brainmask etc however the
command wont work. The command Im suing is
freeview -v wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4
wm1_edits_before/mri/brainmask.mgz \
-f wm1_edits_before/surf/lh.white:edgecolor=blue
wm1_edits_before/surf/lh.pial:e
Hi Freesurfers,
I've recently moved onto Ubuntu 12.04. The Freesurfer installation has
required me to download various libraries and create many symbolic links to
have it working. Further more I've had to set the doublebufferflag=1
(whatever that is) in order for tkmedit and freeview to work (they
Thank you for the almost immediate reply.
Yes, it seems to be otherwise working,
cheers,
Cat
From: Nick Schmansky
To: Cat Chong
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Wednesday, August 29, 2012 2:35 PM
Subject: Re: [Freesurfer] freeview tra
does freeview otherwise appear to be working? that is, does it crash?
the 'invalid drawable' messages can be ignored on the mac.
n.
On Wed, 2012-08-29 at 14:29 -0700, Cat Chong wrote:
>
> Dear Experts:
> I have worked my way through Tracula and things seem to work fine, but
> when I try to
Dear Experts:
I have worked my way through Tracula and
things seem to work fine, but when I try to view my tractography
outputs I get the following persistent error using freeview (copied
below).
I am using a Mac OS X 10.6.7.
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Could this
Hi Inge,
Freeview does not support tcl scripting. It does have lots of
command-line options that might fit your need. Run 'freeview -h" will
display a complete list of the available options.
Best,
Ruopeng
On 6/29/12 7:16 AM, Inge Kasbohm Amlien wrote:
Hi list,
I am looking for a complete re
Hi list,
I am looking for a complete reference to scriptable commands for Freeview,
comparable to what exists for tksurfer (e.g.
http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference)
Does this exist?
Thanks!
___
I
Hi Hiroyuki, can you give us more information? Eg, you click on a given
vertex (col,row,slice), you find the "Scanner RAS" field in tkmedit, you
go to the same col,row,slice in freeview and it's RAS is x,y,z. There
are several different RAS coordinates, and you'll need to be clear as to
which o
Dear Sir,
When I view a brain volume (e.x., orig.mgz) with freeview and tkmedit, RAS
coordinate differs. Why?
Thank you.
Hiroyuki
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Nachricht-
Von: Ruopeng Wang [mailto:rpw...@nmr.mgh.harvard.edu]
Gesendet: Mittwoch, 16. Mai 2012 18:30
An: Focke, Niels
Betreff: Re: AW: [Freesurfer] Freeview chrash
Hi Niels,
Are you using non-English terminals? I think we found the reason. But no fix
yet. The work around is to set your
This is too strange. I logged into the same machine. Both stable and dev
version load the surface file without any problem... We will investigate.
Ruopeng
On 05/03/2012 12:12 PM, Alexandre Gramfort wrote:
>> Alex, since you're in the Martinos center, can you try source the dev
>> version just to
> Alex, since you're in the Martinos center, can you try source the dev
> version just to see if the same problem exists?
I just tried after sourcing /usr/local/freesurfer/nmr-dev-env
and got the same segfault with MatrixMultiply: m2 is null!
I tried on the machine: megmix
Alex
iels Focke
Klinische Neurophysiologie
UMG - Universitätsmedizin Göttingen
-Ursprüngliche Nachricht-
Von: Ruopeng Wang [mailto:rpw...@nmr.mgh.harvard.edu]
Gesendet: Donnerstag, 3. Mai 2012 14:42
An: Alexandre Gramfort
Cc: freesurfer@nmr.mgh.harvard.edu; Focke, Niels
Betreff: Re: [Freesurfer] Freev
<mailto:ta...@mpibpc.mpg.de>
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ruopeng Wang
Sent: Thursday, May 03, 2012 2:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freeview scripting
The text file is just li
The text file is just lines of freeview command-line options for
convenience. It cannot include shell commands.
Ruopeng
On 5/3/12 5:47 AM, Auer, Tibor wrote:
Hi,
I am looking for an option to script freeview as I could tksurfer via
TCL.
I checked the command-line options, and there is a "
Strange. I could not reproduce the error. Niels, I also tried the
surface file you sent me. It loads fine. My colleague could not
reproduce it on his machine, either.
Alex, since you're in the Martinos center, can you try source the dev
version just to see if the same problem exists?
Thanks,
R
Hi,
a bit connecting to my previous mail:
How can I overlay an FSL activation map onto the surface in FreeView? The
solution working in tksurfer (i.e. overlay) is not working here. I can load
the data as a volume, but then it is not projected to the surface.
Thanks,
Auer, Tibor M.D. Ph
Hi,
I am looking for an option to script freeview as I could tksurfer via TCL.
I checked the command-line options, and there is a "-cmd Load freeview
commands from a text file", but I could not find any documentation about the
language/syntax/commands.
Could someone tell me, where can I find
Dear Ruopeng,
to reproduce the problem with :
MatrixMultiply: m2 is null! and the seg fault.
$source /usr/local/freesurfer/nmr-stable51-env
$cd ~gramfort/cluster/work/data/MNE-sample-data/subjects
$setenv SUBJECTS_DIR $PWD
$freeview -f sample/surf/lh.inflated
if you cannot access this folder yo
Dear Ruopeng,
this happens with any surface, for example "bert" lh/rh.pial (that comes with
Freesurfer). I have attached a locally generated surface as well, but I would
guess that the problem is not the surface (files) but rather freeview itself
or an incompatibility maybe with the Centos 5 libra
Would it be possible to send us the surface file that caused the crash?
So that we can replicate the problem?
Thanks,
Ruopeng
On 5/2/12 9:35 AM, Focke, Niels wrote:
> Dear experts,
>
> I have experienced some problems with freeview. When loading a surface (both
> for my locally generated surface
Dear experts,
I have experienced some problems with freeview. When loading a surface (both
for my locally generated surfaces as well as for "bert" surfaces) the program
exits (progress bar at approx. 10%) with this message:
MatrixMultiply: m2 is null!
The problem happens both for command line lo
Hi Freesurfers,
I just want to check my observation that Freeview can not currently be used
for editing the WM.mgz or the brainmask.mgz (for minor skull strip errors)
as is done in TKmedit (cf., Edit Tutorial). Is that correct?
I can’t find any documentation on this, and whilst I would assume
I'm a newbie with FreSurfer and Linux. I'm following Longitudinal
Processing-Tutorial. now I have only files of tutorial data set and I don't
have any other file to test. I can run Freeview and I can load volume from
terminal and from interface, but when I try to load surfaces (from
terminal with
Would it be possible to send us the surface file that crashes freeview?
Ruopeng
On 4/13/12 10:06 AM, carlo cotugno wrote:
I'm a newbie with FreSurfer and Linux. I'm following Longitudinal
Processing-Tutorial. now I have only files of tutorial data set and I
don't have any other file to test. I
I'm a newbie with FreSurfer and Linux. I'm following Longitudinal
Processing-Tutorial. now I have only files of tutorial data set and I don't
have any other file to test. I can run Freeview and I can load volume from
terminal and from interface, but when I try to load surfaces (from
terminal with
Does this happen with every volume you load or just that specific one?
What happens if you change slices? Are you viewing it in the 3D view?
Ruopeng
On 4/13/12 3:34 AM, carlo cotugno wrote:
Dear FreeSurfer experts,
I'm sorry but I have another problem..now when I load a surface (freeview
Hi Carlo
that command line loads a volume, not a surface. Do you load the surface
from the interface? You can do it from the command line with -f name>. Not sure about your problem, but we'll need more details about what
you did
cheers
Bruce
On Fri, 13 Apr 2012, carlo cotugno wrote:
Dear
You can make a copy of the LUT and remove all regions from it you don't want to
see. Then when you load you volume, specify you want to use this new LUT and
you will only see the ROIs in it.
Allison
On Apr 12, 2012, at 11:40 PM, Adil Javed wrote:
> Hi,
> is there any way to overlay only certai
Dear FreeSurfer experts,
> I'm sorry but I have another problem..now when I load a surface (freeview -v
> OAS2_0001_MR1.long.OAS2_0001/mri/norm.mgz)Freeview starts but i can't see the
> image and only when I change for example values in opacity or window, the
> image appears but immediately di
Hi,
is there any way to overlay only certain regions of interest from the LUT table
and not all of them in freeview or tkmedit over a T1 image? I want to just
display certain areas or ROIs.
thanks,
AJ
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what is your command line? Make you you use -f before the surface name so
it knows you are loading a surface. Also, please send us the info we need
to help you! Command line, operating system, terminal output, FS version,
etc
cheers
Bruce
On Thu, 12 Apr 2012, Domenico M.
Mezzapesa wrote:
What version of freesurfer are you running? Would it be possible to send
us the surface file that crashed it?
Ruopeng
On 4/12/12 5:12 AM, Domenico M. Mezzapesa wrote:
> Dear FreeSurfer experts,
>
> I have a problem using FreeView: it can load
> volume without problems, but when I try to load sur
Dear FreeSurfer experts,
I have a problem using FreeView: it can load
volume without problems, but when I try to load surface it crash.
The
error is:
MatrixMultiply: m2 is null!
No such file or directory
Best
regards
Domenico M Mezzapesa
Invita i tuoi amici e Tiscali ti premia! Il consi
Hi all,
I have a question about controlling freeview from the command line.
I would like to overlay some z-score maps for individual subjects on the
fsaverage inflated surface. I would like to use the 'color wheel' color
scale setting and threshold the images between -1 and 1 standard deviations
According to freesurfer release notes
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes, Freeview in
version 5.0 does not work on Snow Leopard. Version 5.1 has fixed it.
Ruopeng
On 04/10/2012 04:36 PM, Jeni Chen wrote:
Hi,
I was recently at the FreeSurfer workshop in Boston and learned a
Hi,
I was recently at the FreeSurfer workshop in Boston and learned about the
"Freeview" tool in Freesurfer. However, when I tried to run it from my own
laptop (Mac book pro), it crashes and gives the error message: "Bus error". I
didn't get a chance to have this problem solved while I was the
Unfortunately no. I'll update it in the next release.
Ruopeng
On 3/4/12 9:11 PM, Blazey, Tyler wrote:
> Hi,
>
> Is there any way to prevent the NIH color map in Freeview from displaying
> values higher than the max as black? I can only seem to find this option for
> the Heat color map.
>
> Than
Hi,
Is there any way to prevent the NIH color map in Freeview from displaying
values higher than the max as black? I can only seem to find this option for
the Heat color map.
Thanks for any help,
-Tyler
The material in this message is private and may contain
Hi Tina
this is easiest to do in tksurfer using the path drawing and custom fill
stuff
cheers
Bruce
On Thu, 16 Feb 2012, Tina Jeon wrote:
Dear freesurfer experts,
I am new to the freeview interface. How do I go about drawing a ROI on the
surfaces to create my own label? Both the voxel e
Dear freesurfer experts,
I am new to the freeview interface. How do I go about drawing a ROI on the
surfaces to create my own label? Both the voxel edit and ROI edit buttons are
not useful in this case.
Thank you in advance,
Tina Jeon
PhD Candidate
Advanced Imaging Research Center
UT Southweste
Hi Holger,
Merry Christmas to you! The labels look ok to me. You have to be careful
looking at a label overlaid on a slice as you are looking at an arbitrary
2d cut through a folded 3d surface. Try viewing the on the inflated surface
in tksurfer and see if they make more sense to you.
Bruce
sure, you can probably just email it to me and Ruopeng. Does it work of you
just load it with -f without the other options?
On Fri, 9 Dec 2011,
Xinian Zuo wrote:
> Thanks, Bruce! The command line is:
>
> freeview --viewsize 500 500 -viewport coronal -slice 1 1 64 -ss
> coronal.64.png -v
> beijin
Thanks, Bruce! The command line is:
freeview --viewsize 500 500 -viewport coronal -slice 1 1 64 -ss
coronal.64.png -v
beijing180/2929166/mri/norm/mgz:opacity=1:grayscale=0,137 -f
beijing180/2929166/surf/lh.white:edgecolor=red -f
beijing180/2929166/surf/rh.white:edgecolor=red
This cmd worked for a
H,
I think the warning message says itself very clear :-). If you load a
volume after the surface, it might not align with it because of the lack
of geometry information in the surface header.
I'm not sure about your second question. Anyone?
Ruopeng
On 12/8/11 3:56 PM, kelsi wrote:
Hi,
wh
Hi,
when I load my ?h.white, inflated, pial, etc data in freeview, I keep
getting this message:
"Surface does not contain valid volume geometry information. It may not
align with volumes and other surfaces"
My command is:
freeview -v fsaverage/mri/aparc+aseg.mgz -f fsaverage/surf/lh.inflated
Would be hard for us to diagnose if we can't replicate the issue. Is
there any core dump file or some kind of log file that may provide any
hint? From what you described, it seems freeview crashes right when it
is about to render the loaded image. that's about as far as I can guess
now. Is that
Hi,
I have not used freeview before in any version. The images open in
tkmedit. What can we do to diagnose this problem?
Xin
On Thu, Dec 8, 2011 at 3:16 PM, Ruopeng Wang wrote:
> I have no problem loading this file in freeview, in both old and new
> versions. Have you used freeview before on th
I have no problem loading this file in freeview, in both old and new
versions. Have you used freeview before on the same system? Did it work?
Ruopeng
On 12/08/2011 02:33 PM, Xin Zheng wrote:
> Hi Ruopeng,
>
> It seems to be with all files. Attached is one of them.
>
> Thanks!
> Xin
>
> On Thu, D
can you open it in tkmedit? Sounds like something is wrong with the file
On
Thu, 8 Dec 2011, Xin Zheng wrote:
> Hi,
>
> We are trying to open something using freeview (ie. freeview -v
> SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
> When we tried to open it directly from t
Does it happen with just that file or with other files as well? Would it
be possible to send us that volume file?
Ruopeng
On 12/08/2011 02:03 PM, Xin Zheng wrote:
> Hi,
>
> We are trying to open something using freeview (ie. freeview -v
> SubjectID_template/mri/norm.mgz) and would get a segmenta
Hi,
We are trying to open something using freeview (ie. freeview -v
SubjectID_template/mri/norm.mgz) and would get a segmentation fault.
When we tried to open it directly from the freeview GUI, it will load
to about 7% and segmentation fault would occur again. We're using
Freesurfer 5.1.0 on Fedor
can you send us your command line? And does this happen right away, or
after you do something in the interface?
cheers
Bruce
On Thu, 8 Dec 2011, Xinian Zuo wrote:
> Freesurfers,
>
> Anyone saw some errors below from FreeView?
> -error
> mess
Freesurfers,
Anyone saw some errors below from FreeView?
-error
message--
freeview.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion
`a[j].inputstride == vptr->stride' failed.
--
Hi Matt
Could you please send information about what Freeview output before it
crash. You could try to run strace freeview to se what is wrong. You
could also add if you are using Linux or Mac Os X.
Knut J
On 08/08/2011 01:41 PM, Hoptman, Matthew wrote:
>
> Hi Ruopeg,
>
> No, glxgears doesn't cr
Hi Ruopeg,
No, glxgears doesn't crash. I'm getting about 3929 FPS.
Thanks,
Matt
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Hi guys,
I've got a list of fiducials (fcsv) from 3DSlicer, Is there a way to
import them within freeview? Those points look like
label,x,y,z,[flag],[flag]
i.e.
P,57.799,-49.1799,13.07,1,1
P,-4.05607,-47.1519,8.93645,1,1
thank in advance.
g.
___
F
Hi Maria,
The fix is done and should be available in tomorrow's dev build.
Ruopeng
On 06/27/2011 12:13 PM, iac...@nmr.mgh.harvard.edu wrote:
> Hi all,
>
> I haven't had any answer to my post, so I give another try. Hope it
> doesn't bother you.
>
> I am trying to overlay a map on a specific su
Hi Maria,
I've tested the files you sent me and were able to replicate the
problem. Will work on it asap. Sorry about the delay.
Ruopeng
On 06/27/2011 12:13 PM, iac...@nmr.mgh.harvard.edu wrote:
> Hi all,
>
> I haven't had any answer to my post, so I give another try. Hope it
> doesn't bother
Hi all,
I haven't had any answer to my post, so I give another try. Hope it
doesn't bother you.
I am trying to overlay a map on a specific subcortical structure (the
caudate).
-I obtained the surface of the structure using the command:
mri_tessellate structure.nii.gz 1 lh.structure.surf
-then
1. is your installation 64b? is there a libXss.so in your /usr/lib64
dir?
2. was this run from scratch or rerun? if rerun, when was wm.mgz
created and by what release? if created by a 5.1beta release late march
to early april, it could have a bug responsible for this. if so, try
rerunning wit
Can you email me one of the wm.mgz volume that fails?
On Wed, 1 Jun 2011, von Polier, Georg
Ferdinand Anto wrote:
> Hi,
>
> using FS 5.1 now, I encountered two problems:
>
> 1. when I try to start freeview on my personal laptop, this errors appears:
>
> [georg@localhost ~]$ freeview
> freeview.bi
Hi,
using FS 5.1 now, I encountered two problems:
1. when I try to start freeview on my personal laptop, this errors appears:
[georg@localhost ~]$ freeview
freeview.bin: error while loading shared libraries: libXss.so.1: cannot open
shared object file: No such file or directory
However, lib
You can try use the flood-fill tool to fill the ROI you outlined.
On 5/16/11 5:58 PM, Lynette Silva wrote:
> Thanks Ruopeng,
>
> I tried tracing the outline with the freehand tool, and I also tried
> setting waypoints around the surface area of my ROI. What tools would
> you recommend?
>
> Thanks
Thanks Ruopeng,
I tried tracing the outline with the freehand tool, and I also tried
setting waypoints around the surface area of my ROI. What tools would
you recommend?
Thanks again!
Lynette
On Mon, May 16, 2011 at 3:46 PM, Ruopeng wrote:
> When you say tracing an ROI by hand in freeview, did
When you say tracing an ROI by hand in freeview, did you fill it or just
traced the outline? In any case, you will need to do this on each slice
by hand. However, there're various options and tools in freeview that
may help speed up the process dramatically.
Ruopeng
On 5/16/11 5:12 PM, Lynette
Hello All,
I think I am missing a key step in creating an ROI in freeview. I have
been tracing an ROI by hand in freeview, and saving as a label. Then I
use mri_label2vol followed by mri_label_volume, and this works
GREAT... except the output has far too few voxels to be the whole
volume of my ROI
Hello all!
I have a question regarding using freeview.
When doing a 3D rengering of t-maps, there is a setting that allows you to
view clusters with peak t scores. When we do this peak t scores are
included in two clusters. We wish to only show ONE cluster for an image
we are creating. How doe
p.s. or you could create a segmentation volume and your own color lut I
guess
On Thu, 5 May 2011, Gabriele Arnulfo wrote:
> Dear freesurfer experts,
>
> I'm currently using freeview to visualize surfaces and volumes. I'm
> wondering if there's a possibility to assign to each control point a
> lab
Hi Gabriele,
I think you want them each to be ROIs then, not control points.
cheers
Bruce
On Thu, 5
May 2011, Gabriele Arnulfo wrote:
> Dear freesurfer experts,
>
> I'm currently using freeview to visualize surfaces and volumes. I'm
> wondering if there's a possibility to assign to each control
Dear freesurfer experts,
I'm currently using freeview to visualize surfaces and volumes. I'm
wondering if there's a possibility to assign to each control point a
label.
My control points are contacts of linear-intra-cerebral electrodes and I
would like to assign a name to each control points in o
You should be able to pick any location you want to save control point,
when the file dialog shows up.
As to default filename, there is no option to set it in freeview now.
But I believe you only need to manually enter file name the first time
you save it.
Ruopeng
On 2/4/11 6:47 PM, Bruce Fis
1. it definitely has to have thatt file name/location for recon-all to
find it.
I'll leave 2 and 3 for Ruopeng
On Fri, 4 Feb 2011, Mehul Sampat wrote:
> Hi Folks,
>
> We used to use tkmedit to add control points and recently started using
> freeview.
> I have a few basic questions about saving c
Hi Folks,
We used to use tkmedit to add control points and recently started using
freeview.
I have a few basic questions about saving controls points created with
freeview.
1. I noticed that in tkmedit edit controls points were saved as
"control.dat" in the "subject_dir"/tmp (e.g. bert/tmp).
When
ory for Advanced Medical Image Processing
> Department of Radiology
> Las Condes Clinic
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl
>
>
> El 18-11-2010 15:57, Gonzalo Rojas escribió:
> > Message: 4
>
0500
> From: Ruopeng Wang
> Subject: Re: [Freesurfer] freeview load overlay error...
> To: freesurfer@nmr.mgh.harvard.edu
>
> What does mris_info show on the overlay file?
>
> On 11/14/10 11:08 PM, Gonzalo Rojas Costa wrote:
>> Hi:
>>
>>I generated a
What does mris_info show on the overlay file?
On 11/14/10 11:08 PM, Gonzalo Rojas Costa wrote:
Hi:
I generated a surface with:
mri_vol2surf --src zstat3.nii.gz --src_type nifti --srcreg ../registro.dat
--hemi lh --projfrac 0.5 --out ./zstat3_lh.w --out_type w
then I tried to load zstat3_lh
it does not work in v5.0. however, this is one of our top priorities to
get working for release in the upcoming 5.1 (within a month or less).
n.
On Fri, 2010-10-22 at 12:42 +0200, Andreas Schindler wrote:
> Dear Freesurfers
>
>
>
> Does anyone know if freeview already works on Mac OS Snow Le
Dear Freesurfers
Does anyone know if freeview already works on Mac OS Snow Leopard or
when it will be patched?
best wishes
Andreas
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Hi,
Annotation option is not available in the stable release version. If you
are able to run the development version, you can load annotation file
from the Surface control panel on the left. Or you can load it from the
command-line like:
freeview -f surface_filename:annot=annotation_filename
Bes
Dear freesurfer experts,I would like to use freeview to check the pial surface and label with annotation file. how to do it ?thanks your helpbestJL--- 本郵件來自HiNet WebMail ---___
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https://mail.nmr.mgh.ha
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
Hi Guys,
Is it possible to get Freeview compiled for a Mac? Last time I check,
it wasn't supported, but it would be of great help to me and at least a
couple other members of my lab. Thanks.
Best,
Jon
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Freesurfer@nmr.mgh.h
Hi,
I have a quick question: has freeview been compiled for an intel
macbook pro?
Thanks,
Jon
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