[Freesurfer] installing on ubuntu

[Ahmed, F, Me]

Hello.

I am going to attempt to install FS on Ubuntu, but just had a quick question 
before I start. On the Download page on the wiki site, it states the following:


On Ubuntu, you will need to do the following:
cd /usr/lib
ln -s libtiff.so.4 libtiff.so.3

When exactly does this need to be done? I know this probably sounds like a 
really stupid question, but I have had major issues with installing FS and want 
to make sure I know exactly what needs doing and when it needs to be done. So 
I'd really appreciate some insight. Thank you.

Kind regards,
Fatima


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Re: [Freesurfer] installing on ubuntu

[Matt Glasser]

Just do it before you try to run any of the FreeSurfer programs.  What
issues are you having?  I have FreeSurfer installed on a number of Ubuntu
machines.

 

Peace,

 

Matt.

 

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ahmed, F, Me

Sent: Monday, August 24, 2009 5:21 AM
To: Freesurfer Mailing List
Subject: [Freesurfer] installing on ubuntu

 

Hello.

 

I am going to attempt to install FS on Ubuntu, but just had a quick question
before I start. On the Download page on the wiki site, it states the
following: 

 

On Ubuntu, you will need to do the following: 

cd /usr/lib

ln -s libtiff.so.4 libtiff.so.3

 

When exactly does this need to be done? I know this probably sounds like a
really stupid question, but I have had major issues with installing FS and
want to make sure I know exactly what needs doing and when it needs to be
done. So I'd really appreciate some insight. Thank you. 

 

Kind regards,

Fatima 

 

 

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Re: [Freesurfer] installing on ubuntu

[Ahmed, F, Me]

Hi Matt,

The problems I've been having with Freesurfer are endless lol. I can't figure 
out how to get it installed on my CentOS Linux. The tar.gz extraction doesn't 
work so I can't get it installed.
So, that command doesn't have to be used in installation? I am SO bad at Linux 
it's unbelievable. Thanks for that though.

Fatima

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
Sent: 24 August 2009 14:31
To: fah...@sun.ac.za
Cc: 'Freesurfer Mailing List'
Subject: Re: [Freesurfer] installing on ubuntu

Just do it before you try to run any of the FreeSurfer programs.  What issues 
are you having?  I have FreeSurfer installed on a number of Ubuntu machines.

Peace,

Matt.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ahmed, F, Me 

Sent: Monday, August 24, 2009 5:21 AM
To: Freesurfer Mailing List
Subject: [Freesurfer] installing on ubuntu

Hello.

I am going to attempt to install FS on Ubuntu, but just had a quick question 
before I start. On the Download page on the wiki site, it states the following:

On Ubuntu, you will need to do the following:
cd /usr/lib
ln -s libtiff.so.4 libtiff.so.3

When exactly does this need to be done? I know this probably sounds like a 
really stupid question, but I have had major issues with installing FS and want 
to make sure I know exactly what needs doing and when it needs to be done. So 
I'd really appreciate some insight. Thank you.

Kind regards,
Fatima


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Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9

[Guang Zeng]

Hi, there,

Could you tell me what I need to unpack to solve the "redraw fails" problem? 

Thanks a lot!

Guang

> > if I recall correctly "the sliver problem" stems from the use of an  
> > incompatible libGL. I did the following that a colleague found out:
> > add the following line to ${FREESURFER_HOME}/bin/tksurfer (that is  
> > the script that calls tksurfer.bin):
> > setenv LD_PRELOAD ${FREESURFER_HOME}bin/libGL.so.1
> >
> > Also unpack the following to reside in your ${FREESURFER_HOME}/bin  
> > directory:
> >
> >
> >
> >
> > (Those are GL libraries from a redhat 4 / centos 4 system that seem  
> > to work with tksurfer).



> From: sebastian.moel...@lur.rwth-aachen.de
> To: corinna...@gmail.com
> Subject: Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9
> Date: Mon, 10 Aug 2009 11:36:21 -0700
> CC: freesurfer@nmr.mgh.harvard.edu; freesurfer...@hotmail.com; 
> ni...@nmr.mgh.harvard.edu
> 
> Hi,
> 
> it seems that my fix is not universal.. Do you see anything at all? In  
> my case I use NX remote controlling on red hat enterprise linux server  
> with the described fix. NX on 32 bit windows works as does Macosx,  
> only Vista 64bit clients running NX to log into the server fail to use  
> double buffering (they do display everything in tksurfer though just  
> really slow). Hmm, I have no real idea what might be going on there,  
> sorry...
> 
> Sebastian
> 
> On Aug 10, 2009, at 11:06 AM, corinna bauer wrote:
> 
> > Hello,
> >
> > I also received the same error message as Guang when trying to run  
> > tksurfer. I added the suggested line to $FREESURFER_HOME/bin/ 
> > tksurfer and unpacked the files, but I still get the following error  
> > message:
> >
> > surfer: current subjects dir: /home/freesurfer4.4.0/subjects/corinna/ 
> > ADNI
> > surfer: not in "scripts" dir ==> using cwd for session root
> > surfer: session root data dir ($session) set to:
> > surfer: /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057
> > surfer: Reading header info from /home/freesurfer4.4.0/subjects/ 
> > corinna/ADNI/003_S_1057/mri/T1.mgz
> > surfer: vertices=116670, faces=26
> > Loading /home/freesurfer4.4.0/surface_labels.txt
> > surfer: ### redraw failed: no gl window open
> > surfer: single buffered window
> > surfer: tkoInitWindow(003_S_1057)
> > surfer: using interface /home/freesurfer4.4.0/lib/tcl/tksurfer.tcl
> > Reading /home/freesurfer4.4.0/lib/tcl/tkm_common.tcl
> > Reading /home/freesurfer4.4.0/lib/tcl/tkm_wrappers.tcl
> > Reading /home/freesurfer4.4.0/lib/tcl/fsgdfPlot.tcl
> > Reading /home/freesurfer4.4.0/lib/tcl/tkUtils.tcl
> > Successfully parsed tksurfer.tcl
> > reading white matter vertex locations...
> >
> > I also tried setenv doublebufferflag 0, which also did not work.
> >
> > Thanks,
> >
> > Corinna
> >
> > On Wed, Aug 5, 2009 at 1:05 PM, Sebastian Moeller 
> >  > > wrote:
> > Hi Guang,
> >
> > if I recall correctly "the sliver problem" stems from the use of an  
> > incompatible libGL. I did the following that a colleague found out:
> > add the following line to ${FREESURFER_HOME}/bin/tksurfer (that is  
> > the script that calls tksurfer.bin):
> > setenv LD_PRELOAD ${FREESURFER_HOME}bin/libGL.so.1
> >
> > Also unpack the following to reside in your ${FREESURFER_HOME}/bin  
> > directory:
> >
> >
> >
> >
> > (Those are GL libraries from a redhat 4 / centos 4 system that seem  
> > to work with tksurfer).
> >
> >
> > Nick, do you think it would be possible to make this change for the  
> > distribution (it was inspired by your inclusion of libGlut to begin  
> > with).
> >
> > ahoi & good luck
> >Sebastian
> >
> >
> > On Aug 5, 2009, at 7:22 AM, freesurfer-requ...@nmr.mgh.harvard.edu  
> > wrote:
> >
> > Date: Wed, 5 Aug 2009 08:49:15 -0500
> > From: Guang Zeng 
> > Subject: [Freesurfer] "redraw failed: no gl window open" problem
> > To: 
> > Message-ID: 
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> > Hi, there,
> >
> > I am running the tksurfer command to view the cortical surface data  
> > as tksurfer bert lh inflated. But I met a problem.
> > I only can view a sliver part of the brain. This sliver portion can  
> > rotate and do everything that tksurfer is supposed to do,
> > but I can't view any more of the brain than a tiny piece. Tkmedit  
> > works fine.
> >
> > When I run the command, it gave me something like this:
> >
> > surfer: current subjects dir: /home/m047599/freesurfer-install/ 
> > freesurfer/subjects
> > surfer: not in "scripts" dir ==> using cwd for session root
> > surfer: session root data dir ($session) set to:
> > surfer: /home/m047599/freesurfer-install/freesurfer
> > surfer: Reading header info from /home/m047599/freesurfer-install/ 
> > freesurfer/subjects/bert/mri/T1.mgz
> > surfer: vertices=131369, faces=262734
> > Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt
> > surfer: ### redraw failed: no gl window open
> > surfer: single buffered window
> > surfer: tkoInitWindow(bert)
> > surfer: using int

Re: [Freesurfer] installing on ubuntu

[Rudolph Pienaar]

Ahmed, F, Me  wrote:
>  
> On Ubuntu, you will need to do the following:
> cd /usr/lib
> ln -s libtiff.so.4 libtiff.so.3
>  

Actually, you should probably use:

sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/lib/tiff.so.3

(it amounts to the same thing, but this way is just one line that you 
can simply cut-and-paste. The system will prompt you for your password.

Also the 'ubuntu' way is to use 'sudo' for administrator-type 
operations. If you just use the above, you will probably get 'Permission 
denied errors').

Note that you *might* get other missing dependencies -- especially if 
you are on a freshly installed ubuntu machine. They are relatively easy 
to resolve using 'apt-get'

> When exactly does this need to be done? I know this probably sounds like 
> a really stupid question, but I have had major issues with installing FS 
> and want to make sure I know exactly what needs doing and when it needs 
> to be done. So I’d really appreciate some insight. Thank you.
>  

It doesn't matter when you do it -- either before or after you unpack 
the archive. Just make sure to do it before you actually run any 
FreeSurfer GUI type apps. If you forget to do it, you'll simply get an 
error along the lines of 'libtiff.so.3 not found'



-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] installing on ubuntu

[Matt Glasser]

I assume you meant sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Rudolph Pienaar
Sent: Monday, August 24, 2009 10:04 AM
To: Ahmed, F, Me 
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] installing on ubuntu

Ahmed, F, Me  wrote:
>  
> On Ubuntu, you will need to do the following:
> cd /usr/lib
> ln -s libtiff.so.4 libtiff.so.3
>  

Actually, you should probably use:

sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/lib/tiff.so.3

(it amounts to the same thing, but this way is just one line that you 
can simply cut-and-paste. The system will prompt you for your password.

Also the 'ubuntu' way is to use 'sudo' for administrator-type 
operations. If you just use the above, you will probably get 'Permission 
denied errors').

Note that you *might* get other missing dependencies -- especially if 
you are on a freshly installed ubuntu machine. They are relatively easy 
to resolve using 'apt-get'

> When exactly does this need to be done? I know this probably sounds like 
> a really stupid question, but I have had major issues with installing FS 
> and want to make sure I know exactly what needs doing and when it needs 
> to be done. So I'd really appreciate some insight. Thank you.
>  

It doesn't matter when you do it -- either before or after you unpack 
the archive. Just make sure to do it before you actually run any 
FreeSurfer GUI type apps. If you forget to do it, you'll simply get an 
error along the lines of 'libtiff.so.3 not found'



-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] installing on ubuntu

[Rudolph Pienaar]

Matt Glasser wrote:
> I assume you meant sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3

Yes - thanks!

-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] mri_surfcluster with qdecs sig.mgh file

[Douglas N Greve]

If you want p-values for the clusters, then you need to run a simulation 
(mri_glmfit-sim). I think QDEC creates a script to do it.

doug

Rosa Steimke wrote:
> dear freesurfer experts. i have another problem in generating output useing 
> mr_surfcluster command. 
>
> i was wondering how to generate an output with the significant clusters from 
> my qdec analysis i learnd that i have to use the mri_surfcluster command and 
> use the sig.mgh file from my qdec. however i am very uncertain about how to 
> apply the explanation (from freesurfer wiki) of the mri_surfcluster commands 
> to the sig.mgh.  i got the error message that the --sum command cannot be 
> used for the sig.mgh file and i dont understand whether i have to apply more 
> commands (besids thresholding, subjects and such) to generate the and output 
> that gives me the size, significant values and coordinates of each of the 
> clusters i can see in qdec. 
>
> thanks for your help. rosa
>   

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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Re: [Freesurfer] installing on ubuntu

[Nick Schmansky]

Fatima,

The current release, v4.5.0, no longer requires performing the 'libtiff'
link.
What other issues are you encountering?

Nick


On Mon, 2009-08-24 at 12:20 +0200, Ahmed, F, Me wrote:
> Hello.
>  
> I am going to attempt to install FS on Ubuntu, but just had a quick
> question before I start. On the Download page on the wiki site, it
> states the following: 
>  
> On Ubuntu, you will need to do the following: 
> cd /usr/lib
> ln -s libtiff.so.4 libtiff.so.3
>  
> When exactly does this need to be done? I know this probably sounds
> like a really stupid question, but I have had major issues with
> installing FS and want to make sure I know exactly what needs doing
> and when it needs to be done. So I’d really appreciate some insight.
> Thank you. 
>  
> Kind regards,
> Fatima 
>  
>  
> ___
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Re: [Freesurfer] fsaverage Talairach Coordinates

[Douglas N Greve]

I actually don't know if your information is out of data. I remember 
years ago we did do some checking on it, and I thought it was accurate 
(can't find my notes not it). If it is not accurate, I would like to 
know. Alternatively, you can report mni305 coordinates.

doug

Matt Leonard wrote:
> Hi Doug,
>
> Thanks for the reply.  I looked at Matthew Brett's transform, which I 
> understand to be a non-linear transform between MNI and Talairach, but 
> I was told that tksurfer's "Talairach" field is not accurate.  Is this 
> simply because Brett's transform is only one of many possible 
> solutions to the problem, or is it because of something else?  Or is 
> my information out of date?  If the Talairach field in tksurfer is 
> accurate enough to report in a paper, then I'm happy to go with that.
>
> Thanks,
>
> Matt
>
>
> On Aug 19, 2009, at 7:11 PM, Douglas N Greve wrote:
>
>> THere are two sets of coordinates that are reportable. First, the 
>> mni305. This is the coordinate system that we use internally (eg, 
>> surface coords of fsaverage are stored in  mni305). We can convert 
>> these coords to "talairach" thru Matthew Brett's transform. This is 
>> what is reported in the "Talairach" field in tkmedit and tksurfer. 
>> Does this answer your question?
>>
>> doug
>>
>> Matt Leonard wrote:
>>> Hi,
>>>
>>> I've been asked to report Talairach coordinates in a paper, but 
>>> I've  been told that the coordinates that are listed on the 
>>> fsaverage brain  (in the talairach.xfm file) are not accurate.  Does 
>>> anyone have a way  to get the true Talairach coordinates on the 
>>> fsaverage brain?
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>> ___
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>>>
>>>
>>>
>
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] thickness map

[Feng-Xian Yan]

2009/8/25 Feng-Xian Yan 

> Hi,
>
>First, I use mri_surf2surf (as follows) to map our subjects to
> fsaverage.
>
> mri_surf2surf –srcsubject subject --sval-tal-xyz white --hemi lh
> --trgsubject fsaverage --tval-xyz --tval lh.subject.tal
>
>
>
> Next step, I use mris_convert to show the cortical thickness value of this
> subject on this MNI coordinates. But, this has an error as follows.
> mris_convert -c subject/surf/lh.thickness fsaverage /surf/lh.white
> lh.subject.thickness.asc
>
>
> ERROR: number of vertices in subject/surf/lh.thickness does not match
> surface  (154962,163842)
>
> I know what’s happen, but I don’t know how to solve.
>
> I want to obtain the asc file containing the same vertices as fsaverage and
> with the cortical thickness value and their coordinates in the file. Could
> you teach me how to obtain the match fsaverage surface file?
>
> Thank you in advance!
>
> Feng-Xian
>
>
>
>
>
>
> 2009/8/20 Bruce Fischl 
>
> you can use mri_surf2surf to map them all the fsaverage, then mris_convert
>> to convert each one to asciii.
>>
>> cheers
>> Bruce
>>
>> On Thu, 20 Aug 2009, Feng-Xian Yan wrote:
>>
>> Hi,
>>>
>>>  But I want to obtain the asc file or other files containing the same
>>> vertices and with the cortical thickness value and their coordinates in
>>> the
>>> file.
>>>
>>> Could some ways to obtain?
>>>
>>>
>>>
>>> Thank you in advance!
>>>
>>>
>>>
>>> Feng-Xian
>>>
>>>
>>>
>>>
>>> 2009/8/20 Doug Greve 
>>>
>>>
 Yes, this is what our group analysis tools do. You can find tutorials
 on the wiki. You'll probably start with mris_preproc.

 doug




 On Thu, 20 Aug 2009, Feng-Xian Yan wrote:

 Hi,

>
>  Thank you for your responses before.
>
>
>
>  I have another problem want to solve. I check the number of vertex for
> all
> subjects, but I found that the number of vertex for each subjects and
> each
> hemispheres is different. Because I want to compare cortical thickness
> using
> vertex-by-vertex, I would to obtain the same vertex number.
>
> Therefore, have something to do to obtain the same vertex number, i.e.
> template the cortical thickness at each vertex for each subject on the
> fsaverage surface, or other methods?
>
>
>
> How can I do? Would you get me a hand?
>
>
>
> Thank you in advance!
>
>
>
> Feng-Xian
>
>
>
>
> 2009/8/18 Feng-Xian Yan 
>
>
> Thank s for your response.
>>
>> So, the coordinates are MNI coordinates, not Talairach coordinates.
>>
>>
>>
>> Thank you in advance.
>>
>>
>>
>> Feng-Xian
>>
>>
>>
>> 2009/8/18 Douglas N Greve 
>>
>> The values in the asc file are in MNI305 space. You can see this in
>>
>>> tksurfer with View->Configure->Information and select the mni305
>>> button.
>>>
>>> Feng-Xian Yan wrote:
>>>
>>>
>>> Thank you for your response.

 So, you mean that I have to do "mris_convert" two times. One for
 lh.white.tal.asc, another for lh.thickness.asc. And the Tal
 coordinates
 in
 lh.white.tal.asc file corresponds to the cortical thickness value in
 lh.thickness.asc file.


 But, the Tal coordinates in lh.white.tal.asc is difference from the
 result in the tksurfer tool box. That is to say, when I open this
 subject by
 tksurfer, I look at the coordinate of the vertex Tal in the tksurfer
 tool
 box, and the coordinate is difference from the coordinates that
 obtain
 from
 the command ?mris_convert ?c lh.thickness lh.white
 lh.thickness.asc?.


 What do have some problems?


 Thank you in advance!


 Feng-Xian


  2009/8/18 Douglas N Greve >>> gr...@nmr.mgh.harvard.edu>>

  You have convert the thickness file (lh.thickness) to ascii like
  you did
  with the surface (with mris_convert). You will then have two
  files, and
  the second file will have the thickness values.

  doug

  Feng-Xian Yan wrote:
 >
 > Hi,
 >
 > Sorry, I don't know what you mean. I know each lines is a vertex
 and
 > represent a Tal coordinate, but each lines only contain xyz, but
 not
 > contain cortical thickness value of these coordinates. That is
  to say,
 > the following is
 >
 > Tal x Tal y Tal z
 >
 > -13.424789 -125.068245 12.671550 0
 >
 > What?s wrong do I think?
 >
 > Thank you in advance.
 >
 > Feng-Xian
 >
 > 2009/8/18 Douglas N Greve >>>  
>>

[Freesurfer] Problem with lgi

[leemon albert]

 Dear all,

I am trying to compute the local gyrification index but unfortunately
encounter the problem below. Matlab Version ( R2007a) and also the Image
Processing Toolbox are installed on my computer (Ubuntu 9.04,32-bit).

I think the matlab isn't rightly called by  the script. But the
"make_outer_surface.m" is not a bash command. Here,  how does it invoke the
Matlab?

Any help is greatly appreciated!

Best wishes,

/mnt/freesurfer/subjects$ recon-all -s dinghai_4 -localGI
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0
INFO: SUBJECTS_DIR is /mnt/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 huiguang huiguang 803627 Aug 25 09:44
/mnt/freesurfer/subjects/dinghai_4/scripts/recon-all.log
Linux hhg-linux 2.6.24-19-generic #1 SMP Wed Aug 20 22:56:21 UTC 2008 i686
GNU/Linux
/mnt/freesurfer/subjects/dinghai_4/surf
#
#...@# Local Gyrification Index lh Tue Aug 25 09:54:08 CST 2009

 mris_compute_lgi --i lh.pial

=
rm -Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
make_outer_surface('/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=
if: Expression Syntax.

ERROR: make_outer_surface did not create output file
'/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Linux hhg-linux 2.6.24-19-generic #1 SMP Wed Aug 20 22:56:21 UTC 2008 i686
GNU/Linux

recon-all exited with ERRORS at Tue Aug 25 09:54:18 CST 2009

Then I open the matlab ,there is a warning: "Executing startup failed in
matlabrc.',...
'This indicates a potentially serious problem in your MATLAB
setup,',...
'which should be resolved as soon as possible. "



-- 
Albert
Lab of Complex System and Artificial Intelligence,
Institute of Automation,Chinese Academy of Sciences(CASIA)
Beijing, 100190,P.R.CHINA
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Re: [Freesurfer] installing on ubuntu

[Feuerstein Philippe]

I just did a fresh install of 4.5.0 on a new machine with an "out of the box" 
Ubuntu 9.04

You still need (at least):

* to create the symbolic link for libtiff
* to install the tcsh package (wich is not by default)

Hope this can help.


---

Dr Philippe Feuerstein
Radiologie
Groupe Hospitalier du Centre Alsace
Hôpital Albert Schweitzer
201, Avenue d'Alsace - BP 20129
68003 Colmar Cedex
France

Tél: +33 3 89 21 25 74


mailto: philippe.feuerst...@ghca.fr



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
Sent: Monday, August 24, 2009 9:20 PM
To: Ahmed, F, Me 
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] installing on ubuntu

Fatima,

The current release, v4.5.0, no longer requires performing the 'libtiff'
link.
What other issues are you encountering?

Nick


On Mon, 2009-08-24 at 12:20 +0200, Ahmed, F, Me wrote:
> Hello.
>
> I am going to attempt to install FS on Ubuntu, but just had a quick
> question before I start. On the Download page on the wiki site, it
> states the following:
>
> On Ubuntu, you will need to do the following:
> cd /usr/lib
> ln -s libtiff.so.4 libtiff.so.3
>
> When exactly does this need to be done? I know this probably sounds
> like a really stupid question, but I have had major issues with
> installing FS and want to make sure I know exactly what needs doing
> and when it needs to be done. So I'd really appreciate some insight.
> Thank you.
>
> Kind regards,
> Fatima
>
>
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