Woo Suk
The function is made for the SPM5 task manager. You cannot run it separately, as all it will do is
output a job structure for spm_jobman. To use it do the following
1) make a directory called extractbrain and put it in spm5/toolbox directory.
2) put the extractbrain.m file inside this directory.
3) if matlab is running, quit matlab (otherwise there may be global variables from spm hanging
around if you had run spm5)
4) restart matlab
5) start spm5
6) look under the Tasks menu -> Tools. You should see an entry called extractbrain. Select it and
you should be ready to go.
let me know if you still have trouble.
Darren
==============Original message text===============
On Mon, 04 Dec 2006 5:32:07 pm CST "Woo Suk, Tae" wrote:
Dear Darren Gitelman.
I really thank you for your reply.
I deleted the brackets {{{ }}}, and I got the following message.
But, there was no other process.
I attached extracted script, would you check it?
Sincerely yours.
Woo Suk, Tae
Seoul, Korea
-----------------------------------------------------------------------
ans =
type: 'branch'
name: 'Skull Strip using BET2'
tag: 'skullstrip'
val: {[1x1 struct] [1x1 struct] [1x1 struct]}
prog: @extbrain
vfiles: @vfiles_extbrain
help: {'Skull strip a brain using bet2.'}
------------------------------------------------------------------------
-----Original Message-----
From: Darren Gitelman [mailto:[log in to unmask]]
Sent: Monday, December 04, 2006 4:13 PM
To: '"Å¿켮"'
Subject: RE: [SPM] skull stripping algorithm...
Make sure that extra characters did not get pasted into the code. The
first line of the function should read
function opts = cbmg_config_extractbrain
Make sure there are no other characters or lines in the function before
this line.
You may have accidentally copied some of the other characters such as curly
brackets {{{ which are only there for the tiddlywiki formatting.
The last line of the function should be the word "return"
Please let me know if this helps.
Darren
-----Original Message-----
From: "Å¿켮" [mailto:[log in to unmask]]
Sent: Sunday, December 03, 2006 6:08 PM
To: [log in to unmask]
Subject: RE: [SPM] skull stripping algorithm...
Dear Darren Gitelman.
I had error message, when I ran BET2 in SPM5.
How can I correct it?
----------------------------------------------------------------------------
--------------------------------------------------------
?? Error: File: c:\spm5\toolbox\extractbrain\cbmg_config_extractbrain.m
Line: 2 Column: 1 Illegal use of reserved keyword "function".
Error in ==> c:\spm2002\spm5\spm.m
On line 1502 ==> evalin('base',xTB(i).prog);
??? Error while evaluating uicontrol Callback.
----------------------------------------------------------------------------
--------------------------------------------------------
Woo Suk, Tae
Seoul, Korea
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]On
Behalf Of Darren Gitelman
Sent: Sunday, December 03, 2006 2:53 PM
To: [log in to unmask]
Subject: Re: [SPM] skull stripping algorithm...
Hi Gonzalo
There is a very nice skull stripping algorithm in the FSL software called
bet2. Download that and you can integrate it within SPM using this function
http://cbmg.tiddlyspot.com/#extractbrain
Darren
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
Behalf Of Gonzalo Rojas
Sent: Saturday, December 02, 2006 3:31 PM
To: [log in to unmask]
Subject: [SPM] skull stripping algorithm...
Hi:
SPM5 have any skull stripping algorithm implemented on it ?...
Sincerely,
Gonzalo Rojas Costa
<http://smc.samsung.co.kr/smcmail/cgi-bin/setconfirm.cgi?k=116519090964080172&u=wstae&d=smc.samsung.co.kr> ===========End of original
message text===========
--------------------------------
Darren R. Gitelman, M.D.
Cognitive Neurology and the Alzheimer's Disease Center
Northwestern Univ., 320 E. Superior St., Searle 11-470, Chicago, IL 60611
Voice: (312) 908-9023 Fax: (312) 908-8789
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