Bet error

Dear Expert:
I have 'sourced ' FSL in the terminal like this:
FSLDIR=/Applications/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
I then inputted the command 'bet' and received below options.

Usage: bet [options]

Then I opened matlab with the following command in the same terminal:
/Applications/MATLAB_R2012b.app/bin/matlab

Unfortunately, I am receiving another error message.
I would appreciate any help.
Very Best Regards,
Cat

Warning: Directory already exists.
In DPARSFA_run at 1155
In DPARSF_run at 95
In DPARSF>pushbuttonRun_Callback at 1117
In gui_mainfcn at 96
In DPARSF at 50
Apply Reorient Mats to functional images for M1003: OK
Apply Reorient Mats to functional images for M1002: OK
Bet begin...
/Applications/fsl/bin/bet: line 150: /bin/remove_ext: No such file or directory
/Applications/fsl/bin/bet: line 151: /bin/remove_ext: No such file or directory
/Applications/fsl/bin/bet: line 153: /bin/imtest: No such file or directory
/Applications/fsl/bin/bet: line 153: [: =: unary operator expected
/Applications/fsl/bin/bet: line 235: /bin/bet2: No such file or directory
/Applications/fsl/bin/bet: line 150: /bin/remove_ext: No such file or directory
/Applications/fsl/bin/bet: line 151: /bin/remove_ext: No such file or directory
/Applications/fsl/bin/bet: line 153: /bin/imtest: No such file or directory
/Applications/fsl/bin/bet: line 153: [: =: unary operator expected
/Applications/fsl/bin/bet: line 235: /bin/bet2: No such file or directory
/Applications/fsl/bin/bet: line 150: /bin/remove_ext: No such file or directory
/Applications/fsl/bin/bet: line 151: /bin/remove_ext: No such file or directory
/Applications/fsl/bin/bet: line 153: /bin/imtest: No such file or directory
/Applications/fsl/bin/bet: line 153: [: =: unary operator expected
/Applications/fsl/bin/bet: line 235: /bin/bet2: No such file or directory
/Applications/fsl/bin/bet: line 150: /bin/remove_ext: No such file or directory
/Applications/fsl/bin/bet: line 151: /bin/remove_ext: No such file or directory
/Applications/fsl/bin/bet: line 153: /bin/imtest: No such file or directory
/Applications/fsl/bin/bet: line 153: [: =: unary operator expected
/Applications/fsl/bin/bet: line 235: /bin/bet2: No such file or directory
Bet finished
Copying T1 image Files:M1003 OKCopying T1 image Files:M1002 OK
Index exceeds matrix dimensions.

Error in DPARSFA_run>(parfor body) (line 1605)
SourceFile=[AutoDataProcessParameter.DataProcessDir,filesep,'T1ImgBet',filesep,AutoDataProcessParameter.SubjectID{i},filesep,SourceDir(1).name];

Error in parallel_function (line 466)
F(base, limit);

Error in DPARSFA_run (line 1548)
parfor i=1:AutoDataProcessParameter.SubjectNum

Error in DPARSF_run (line 95)
[Error] = DPARSFA_run(Cfg);

Error in DPARSF>pushbuttonRun_Callback (line 1117)
[Error]=DPARSF_run(handles.Cfg);

Error in gui_mainfcn (line 96)
feval(varargin{:});

Error in DPARSF (line 50)
gui_mainfcn(gui_State, varargin{:});

Error while evaluating uicontrol Callback

Comments

Hi Cat,

"/Applications/fsl/bin/bet: line 150: /bin/remove_ext: No such file or directory"

I suspect there is something wrong with your FSL installation.

You can test it by bet a T1 image in terminal.

If so, you may try to re-install FSL.

Best,

Chao-Gan

 

Dear Dr. Yan,

Thank you for providing such a useful toolbox for data preprocessing with DPARSF A. It works perfectly now after I reinstalled fsl. 

I have preprocessed all my data with DPARSF I would like to use REST to estimate Functional connectivity.  I have two resting-state sessions, and my data is currently in two folders (FunImgARCFWS for the first resting state run  and S2_FunImgARCFWS for the second resting state run). 

How do I set up the data correctly so that Rest can read that each person had two processed resting state runs?

Thank you very much for your help.

Cheers,

Cat

Hi Cat,

The easiest way is click "Functional Connectivity" and then "Define ROI" in DPARSF, then you will get the functional connectivity maps automatically.

If you want to use REST, you need to do it seperately for  FunImgARCFWS and S2_FunImgARCFWS. You need "add all-subfolders recursively" to add all the subjects.

Best,

Chao-Gan





Thank you very much for your ongoing help it is much appreciated. 
Cheers,
Cat





Dear Expert,

we runned into the same error of Cat: 

/usr/local/fsl/bin/bet: line 151: /bin/remove_ext: No such file or directory

...

but we think that our FSL installation is good because we usually used bet and we also tried to run bet from the terminal with a T1 image and evrything works in the correct way. Could you please let us know how we can find out what is the problem? We are running DPARSF v.3.1

Any help will be appreciated. 

Thanks