A question of running fsfast in mac - Freesurfer

24 May 2013


      Dear Freesurfer experts:
hi, I'm one of the attendees of the multi-modality training program. I had
tried running fsfast in the mac and got an error message. Below is the
detail information. Any of your suggestions is highly appreciated and thank
you very much.
-Sharon
OS: Mac OS X 10.5.6
[YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% pwd
/Users/Young/Desktop/DICOM/13051914
[YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% selxavg3-sess -s
sess01 -analysis
/Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/001/test01.sm05.lh
-no-preproc -c music_silence.mat
--------------------------------------------------------------
selxavg3-sess logfile is
/Users/Young/Desktop/DICOM/13051914/log/selxavg3-sess-bold-test01.sm05.lh-130524090501.log
--------------------------------------------------------------
-------------------------------------------
/Users/Young/Desktop/DICOM/13051914/sess01
Fri May 24 09:05:02 EDT 2013
anadir = /Users/Young/Desktop/DICOM/13051914/sess01/bold/test01.sm05.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a
display.
  You will not be able to display graphics on the screen.
< M A T L A B >
                  Copyright 1984-2007 The MathWorks, Inc.
                         Version 7.4.0.287 (R2007a)
                              January 29, 2007
Warning: Duplicate directory name: /Users/Young/matlab.
Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the
same name as a MATLAB builtin. We suggest you rename the function to avoid
a potential name conflict.
To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the
same name as a MATLAB builtin. We suggest you rename the function to avoid
a potential name conflict.
...
In hgrc at 132
In matlabrc at 105
Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the
same name as a MATLAB builtin. We suggest you rename the function to avoid
a potential name conflict.
...
In path at 110
In startup at 5
  In matlabrc at 255
Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the
same name as a MATLAB builtin. We suggest you rename the function to avoid
a potential name conflict.
...
In path at 110
In startup at 14
  In matlabrc at 255
...
...
...
...
...
...
>> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# sess01 ###############################
/Users/Young/Desktop/DICOM/13051914/sess01
-------------------------
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
/Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/Applications/freesurfer/matlab/MRIread.m
-------------------------
outtop = /Users/Young/Desktop/DICOM/13051914
Extension format = nii.gz
 1 music_silence.mat
??? Error using ==> MRIread at 76
ERROR: cannot determine format of
/Users/Young/Desktop/DICOM/13051914/sess01/bold/001/fmc.siemens.sm5
(MRIread)
Error in ==> flac_customize at 87
mri = MRIread(fstem,1);
Error in ==> fast_selxavg3 at 65
flac0 = flac_customize(flac0);
...
...
2013-05-24 09:05:32.710 MATLAB[65661:60b] Process manager already
initialized -- can't fully enable headless mode.
------------------------------------------
ERROR: fast_selxavg3() failed\n