DPARSF 2.2 error

Submitted by Turk on Fri, 03/15/2013 - 20:18

Submitted by Turk on Fri, 03/22/2013 - 17:43

Hi,
Thanks for your response- and I am sorry as I thought I sent it!
(I am using DPARSF 2.2, Rest 1.8, Matlab 2010a, Spm8 updated)
Here its:

The following modules did not run:
Failed: New Segment
??? Error using ==> cfg_util at 835
Job execution failed. The full log of this run can be found in
MATLAB command window, starting with the lines (look for the
line showing the exact #job as displayed in this error
message)
------------------
Running job #2
------------------
Error in ==> spm_jobman at 217
Error in ==> DPARSFA_run>(parfor body) at 1416
Error in ==> parallel_function at 475
Error in ==> DPARSFA_run at 1393
Error in ==> DPARSFA>pushbuttonRun_Callback at 1569
Error in ==> gui_mainfcn at 96
Error in ==> DPARSFA at 33
??? Error while evaluating uicontrol Callback

Thanks

Turk

Submitted by YAN Chao-Gan on Tue, 03/26/2013 - 04:04

Hi Turk,

Do you have more information? E.g., some lines before these lines?

Possibly is the problem of SPM8 installation.

Best,

Chao-Gan

Submitted by cpehrs on Fri, 04/12/2013 - 21:18

Hi, did you find a solution to your problem? I have similar error messages occuring. I think it's about the versions you use for matlab, SPM, JAVA, Rest and DPARSF. I use Matlab2009b, SPM8, DPARSF 2.2, Rest 1.8, Java SE 6.

Does anybody have more infomation about the compatability of the versions?

I heard DPARSF_V2.2_121225, REST_V1.8_121225, spm8, java7_17, Matlab R2012a is a good match?!

Thanks a lot,

Corinna  

Submitted by Turk on Fri, 04/12/2013 - 21:44

 Hi Corinna,

I did not find any solution for this problem and I am not sure about the compatibility of the DPARSF 2.2 version with other softwares (Matlab, REST and SPM8). As you mentioned it might be compatibility issue as I use  MatlabR2010a, SPM8, DPARSF 2.2, Rest 1.8, Java SE 6. It would be good idea if someone shed light on this issue to clarify it. Thanks

Turk


Submitted by YAN Chao-Gan on Fri, 04/12/2013 - 22:51

Hi,

DPARSF_V2.2_121225, REST_V1.8_121225, spm8, java7_17, Matlab R2012a is a good match.

Now you can use the newest versions:
DPARSF_V2.2_130309, REST_V1.8_130303. They are compatilbe with MATLAB 2008~2012a. 2012b hasn't been fully tested yet, but should not be a problem.

I guess you problem is that you didn't set up SPM8 correctly: please "add with subfolders" for SPM8. For REST and DPARSF, just add folder.

Best,

Chao-Gan


Submitted by cpehrs on Fri, 04/12/2013 - 23:50

Thanks a lot! I changed the matlab path setting accordingly. 
Unfortunately, the error messages persist:

??? Java exception occurred:
java.lang.NullPointerException
at java.util.logging.Logger.demandLogger(Logger.java:286)
at java.util.logging.Logger.getLogger(Logger.java:321)
 
Error in ==> initclient at 46
logger = Logger.getLogger('net.jini');

Note, that I use Java SE6 and a Mac. When I try again to open DPARSF advanced the following error message occurs:

??? Undefined function or variable 'distcomp.interactiveclient'.

It's possible to open the basic edition of DPARSF, but then  after starting the analysis, the following similar error message pops up:

??? Java exception occurred:
java.lang.NullPointerException
at java.util.logging.Logger.demandLogger(Logger.java:286)
at java.util.logging.Logger.getLogger(Logger.java:321)
 
Error in ==> initclient at 46
logger = Logger.getLogger('net.jini');
 
Error in ==> distcomp.schema at 11
initclient;
 
Error in ==> parallel_function at 430
if W > 0 && PCTInstalled && distcomp.remoteparfor.tryRemoteParfor
 
Error in ==> DPARSF_run at 254
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in ==> DPARSF>pushbuttonRun_Callback at 994
    [Error]=DPARSF_run(handles.Cfg);
 
Error in ==> gui_mainfcn at 96
        feval(varargin{:});
 
Error in ==> DPARSF at 47
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback

After starting the analysis again:

The following modules did not run:
Failed: Slice Timing
 
??? Error using ==> cfg_util at 835
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line
showing the exact #job as displayed in this error message)
------------------
Running job #1
------------------
 
 
Error in ==> spm_jobman at 217
 
 
Error in ==> DPARSF_run at 353
 
 
Error in ==> DPARSF>pushbuttonRun_Callback at 994
 
 
Error in ==> gui_mainfcn at 96
 
 
Error in ==> DPARSF at 47
 
 
??? Error while evaluating uicontrol Callback

Help would be much appreciated. 

Best, Corinna

Submitted by YAN Chao-Gan on Sat, 04/13/2013 - 00:10

The first issue is a JAVA issue. Restart or reinstall matlab should adress such an issue. 

The second issue could be the wrong specification of the slice timing parameters. Please check slice number, slice oeder...

Please copy the lines before "The following modules did not run:

Failed: Slice Timing" here.

Best,

Chao-Gan

Submitted by YAN Chao-Gan on Sat, 04/13/2013 - 00:22

Actually, for the java issue, please refer to http://www.restfmri.net/forum/node/1410 to find some information there.

Submitted by cpehrs on Sat, 04/13/2013 - 01:00

 The full lines:

Slice Timing Setup:loe_2119 OKSlice Timing Setup:loe_2122 OKSlice Timing Setup:loe_2123 OKSlice Timing Setup:loe_2124 OKSlice Timing Setup:loe_2134 OKSlice Timing Setup:loe_2135 OKSlice Timing Setup:loe_2137 OKSlice Timing Setup:loe_2143 OKSlice Timing Setup:loe_2144 OKSlice Timing Setup:loe_2145 OKSlice Timing Setup:loe_2151 OKSlice Timing Setup:loe_2155 OKSlice Timing Setup:loe_2156 OKSlice Timing Setup:loe_2160 OKSlice Timing Setup:loe_2163 OKSlice Timing Setup:loe_2164 OKSlice Timing Setup:loe_2165 OKSlice Timing Setup:loe_2166 OKSlice Timing Setup:loe_2172 OKSlice Timing Setup:loe_2183 OKSlice Timing Setup:loe_2194 OKSlice Timing Setup:loe_2203 OKSlice Timing Setup:loe_2292 OKSlice Timing Setup:loe_2293 OKSlice Timing Setup:loe_2294 OKSlice Timing Setup:loe_2416 OKSlice Timing Setup:loe_2438 OKSlice Timing Setup:loe_2439 OK
Warning: Run spm_jobman('initcfg'); beforehand 
> In spm_jobman at 107
  In DPARSF_run at 352
  In DPARSF>pushbuttonRun_Callback at 994
  In gui_mainfcn at 96
  In DPARSF at 47
 
 
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Slice Timing'
 
SPM8: spm_slice_timing (v4310)                     18:56:16 - 12/04/2013
========================================================================
Failed  'Slice Timing'
Index exceeds matrix dimensions.
In file "/Users/corinnapehrs/Documents/spm8/spm_slice_timing.m" (v4310), function "spm_slice_timing" at line 131.
In file "/Users/corinnapehrs/Documents/spm8/config/spm_run_st.m" (v2312), function "spm_run_st" at line 25.
 
The following modules did not run:
Failed: Slice Timing
 
??? Error using ==> cfg_util at 835
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line
showing the exact #job as displayed in this error message)
------------------
Running job #1
------------------
 
 
Error in ==> spm_jobman at 217
 
 
Error in ==> DPARSF_run at 353
 
 
Error in ==> DPARSF>pushbuttonRun_Callback at 994
 
 
Error in ==> gui_mainfcn at 96
 
 
Error in ==> DPARSF at 47
 
 
??? Error while evaluating uicontrol Callback

37 slices, interleaved. Settings: Slice Number: 37, Slice Order: [1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36], Reference Slice: 37. The setting are right as they worked before...?!

Thanks, Corinna 

Submitted by YAN Chao-Gan on Sat, 04/13/2013 - 01:51

Please check the subjects. I guess there are several subjects are not acquired with this slice parameter.

Submitted by cpehrs on Sat, 04/13/2013 - 01:08

 On another macbook with the same set up of versions it's not the java error message, it's:

Reference: Yan C and Zang Y (2010) DPARSF: a MATLAB toolbox for "pipeline" data analysis of resting-state fMRI. Front. Syst. Neurosci. 4:13. doi:10.3389/fnsys.2010.00013;     Song, X.W., Dong, Z.Y., Long, X.Y., Li, S.F., Zuo, X.N., Zhu, C.Z., He, Y., Yan, C.G., Zang, Y.F., 2011. REST: A Toolkit for Resting-State Functional Magnetic Resonance Imaging Data Processing. PLoS ONE 6, e25031.

??? No public field IsStartupComplete exists for class distcomp.interactiveclient.

 

Error in ==> distcomp.interactiveclient.interactiveclient at 11

obj.IsStartupComplete = false;

 

Error in ==> distcomp.pGetInteractiveObject at 33

                conn = distcomp.interactiveclient;

 

Error in ==> distcomp.getInteractiveObject at 11

c = distcomp.pGetInteractiveObject('create');

 

Error in ==> matlabpool at 117

client = distcomp.getInteractiveObject();

 

Error in ==> DPARSFA>DPARSFA_OpeningFcn at 230

            CurrentSize_MatlabPool = matlabpool('size');

 

Error in ==> gui_mainfcn at 221

    feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});

 

Error in ==> DPARSFA at 33

    gui_mainfcn(gui_State, varargin{:});

 

Error in ==> DPARSF>DPARSF_OpeningFcn at 60

        DPARSFA;

 

Error in ==> gui_mainfcn at 221

    feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});

 

Error in ==> DPARSF at 47

    gui_mainfcn(gui_State, varargin{:});

It would be great you'd have an idea about that. 

Cheers, Corinna

Submitted by YAN Chao-Gan on Sat, 04/13/2013 - 01:49

Matlab2009?
The parallel computing toolbox may not work so well in Matlab 2009. I but I don't have such a plotform to test.