dparsf

Submitted by johnsonzhj on Fri, 06/11/2010 - 19:18

Dear Chaogan,

       I want to used the Dparsf to process the domenstration data you released recently, but I come across with the problem blow.
       What is wrong with this? Thank you.

Best,

Johnsonzhj

Converting 128/128  1
0000001.dcm->20070930_0905050000001t1mpragesagSub003s010a1001E.nii
GZip 20070930_0905050000001t1mpragesagSub003s010a1001E.nii
Reorienting as C:\FMRI\RESTINGSTATE\PROCESSINGDEMODATA\T1IMG\SUB_003\o20070930_0905050000001t1mpragesagSub003s010a1001E.nii.gz
GZip o20070930_0905050000001t1mpragesagSub003s010a1001E.nii
Cropping NIfTI/Analyze image C:\FMRI\RESTINGSTATE\PROCESSINGDEMODATA\T1IMG\SUB_003\o20070930_0905050000001t1mpragesagSub003s010a1001E.nii.gz
GZip co20070930_0905050000001t1mpragesagSub003s010a1001E.nii
Time elapsed 12620ms
Converting T1 Images:Sub_003 OK
??? Index exceeds matrix dimensions.

Error in ==> DPARSF_run at 276
            delete(DirImg(j).name);

Error in ==> DPARSF>pushbuttonRun_Callback at 935
    [Error]=DPARSF_run(handles.Cfg);

Error in ==> gui_mainfcn at 96
        feval(varargin{:});

Error in ==> DPARSF at 39
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback
 

Submitted by dongzy08 on Sun, 06/13/2010 - 21:09

The error ' Index exceeds matrix dimensions' told me that in the option 'Remove First n Time Points' , maybe the n you specified is larger than the real number of the time points.

Submitted by johnsonzhj on Mon, 06/14/2010 - 01:34

But I  remeber I just use the default .m flie from the demonstration data.Anyway, I will check this option tomorrow. Thank you.

Submitted by YAN Chao-Gan on Mon, 06/14/2010 - 11:03

Hi!
Please check what do you have under C:\FMRI\RESTINGSTATE\PROCESSINGDEMODATA\FunImg\Sub_003

Submitted by johnsonzhj on Tue, 06/15/2010 - 14:59

真奇怪，我查过了，也重新下载数据解压缩了，问题还是一样存在。不知道是什么原因。
我把第三个被试的数据删了，问题还是存在。期待解答。
SPM5: spm_slice_timing (v$Rev: 671 $)              09:11:35 - 14/06/2010
========================================================================
??? Index exceeds matrix dimensions.

Error in ==> spm_slice_timing at 130
Vin  = spm_vol(P{1}(1,:));

Error in ==> spm_config_slice_timing>slicetiming at 170
    spm_slice_timing(P,Seq,refslice,timing)

Error in ==> spm_jobman>run_struct1 at 1587
        feval(prog,val);

Error in ==> spm_jobman>run_struct1 at 1597
            run_struct1(c.val{i},gui);

Error in ==> spm_jobman>run_struct1 at 1597
            run_struct1(c.val{i},gui);

Error in ==> spm_jobman>run_job at 482
    run_struct1(c,gui);

Error in ==> spm_jobman at 89
            run_job(varargin{2});

Error in ==> DPARSF_run at 315
        spm_jobman('run',jobs);

Error in ==> DPARSF>pushbuttonRun_Callback at 935
    [Error]=DPARSF_run(handles.Cfg);

Error in ==> gui_mainfcn at 96
        feval(varargin{:});

Error in ==> DPARSF at 39
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback

 

Submitted by YAN Chao-Gan on Tue, 06/15/2010 - 17:21

请检查一下C:\FMRI\RESTINGSTATE\PROCESSINGDEMODATA\FunImg\Sub_003 生成了什么文件？

Hi!
Please check what do you have under C:\FMRI\RESTINGSTATE\PROCESSINGDEMODATA\FunImg\Sub_003

Submitted by johnsonzhj on Tue, 06/15/2010 - 22:01

Dear Chaogan,

20070930_0905050000001gefunc31x31x30240RSSub003s004a001.nii.gz
20070930_0905050000001gefunc31x31x30240RSSub003s004a001A.nii.gz
Two files can be found in the filefolder you mentioned.

Best,

Submitted by YAN Chao-Gan on Fri, 06/18/2010 - 16:11

Plese update your DPARSF to the latest version and have another try.

Submitted by johnsonzhj on Fri, 06/18/2010 - 23:25

Dear Chaogan,

                       OK! I will try again.Thank you.

Submitted by johnsonzhj on Fri, 06/18/2010 - 23:46

Dear Chaogan,
 
        Thank you very much for your kind help!
        But I am very sorry to tell you that the problem still exsit.I have coped with this problem for more than one week, it is really weird that I can not solve it.Is there anything wrong with my matlab?

Best wishes,

Submitted by johnsonzhj on Sat, 06/19/2010 - 00:10

我用你提供的例子的数据试了两次还是不行。这次我尝试用一个自己带任务的数据先用MRIconvert转换为NIFTI格式后用dparsf试验的报错结果。好像有点类似。
??? Index exceeds matrix dimensions.

Error in ==> spm_slice_timing at 130
Vin  = spm_vol(P{1}(1,:));

Error in ==> spm_config_slice_timing>slicetiming at 170
    spm_slice_timing(P,Seq,refslice,timing)

Error in ==> spm_jobman>run_struct1 at 1587
        feval(prog,val);

Error in ==> spm_jobman>run_struct1 at 1597
            run_struct1(c.val{i},gui);

Error in ==> spm_jobman>run_struct1 at 1597
            run_struct1(c.val{i},gui);

Error in ==> spm_jobman>run_job at 482
    run_struct1(c,gui);

Error in ==> spm_jobman at 89
            run_job(varargin{2});

Error in ==> DPARSF_run at 315
        spm_jobman('run',jobs);

Error in ==> DPARSF>pushbuttonRun_Callback at 935
    [Error]=DPARSF_run(handles.Cfg);

Error in ==> gui_mainfcn at 96
        feval(varargin{:});

Error in ==> DPARSF at 39
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback

Submitted by YAN Chao-Gan on Sat, 06/19/2010 - 11:12

你的操作系统是Windows Vista或Windows 7吧？
问题出在这里：
20070930_0905050000001gefunc31x31x30240RSSub003s004a001.nii.gz
转格式之后转成.nii.gz　DPARSF是不认的。要求转成SPM5的.hdr/.img格式。
另外，你的DPARSF是什么版本？
在命令行输入一下：
which DPARSF
报告一下结果。另外，启动DPARSF时在命令行窗口有一堆信息，贴上来确认一下。

Submitted by johnsonzhj on Mon, 06/21/2010 - 16:22

对，我现在用的电脑是德文版的windows7系统。Dparsf是我刚从你们网站上重新下的，我周末用不了Matlab，周一在实验室的时候把相关的信息报告给你。
那我要在windows7系统下用Dparsf，应该怎么做呢？
>> which dparsf
C:\fMRI\software\DPARSF_V1.0_100510\DPARSF.m

Warning: Could not find an exact (case-sensitive) match for 'dparsf'.
C:\fMRI\software\DPARSF_V1.0_100510\DPARSF.m is a case-insensitive match and will be used
instead.
You can improve the performance of your code by using exact
name matches and we therefore recommend that you update your
usage accordingly. Alternatively, you can disable this warning using
warning('off','MATLAB:dispatcher:InexactCaseMatch').
This warning will become an error in future releases.
Welcome: Johnsonzhj, 2010-06-21 08:14
Data Processing Assistant for Resting-State fMRI (DPARSF). Release=V1.0_100510
Copyright(c) 2009~2012
State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, China
Mail to Author:  YAN Chao-Gan
http://www.restfmri.net
-----------------------------------------------------------
Citing Information:
If you think DPARSF is useful for your work, citing it in your paper would be greatly appreciated.
Something like "... preprocessing were carried out using Statistical Parametric Mapping (SPM5, http://www.fil.ion.ucl.ac.uk/spm) and Data Processing Assistant for Resting-State fMRI (DPARSF) (Yan and Zang, 2010) ..." in your method session would be fine. If FC, ReHo, ALFF or fALFF is computed, please also cite Resting-State fMRI Data Analysis Toolkit (REST, by Song et al., http://www.restfmri.net).
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

Submitted by YAN Chao-Gan on Mon, 06/21/2010 - 17:26

如果DPARSF不能正确地将数据转为SPM5的.hdr/.img格式，那你用其他的工具先转格式再用DPARSF。
可以用SPM8或MRIcroN来转。具体可以参照视频。

Submitted by johnsonzhj on Tue, 06/22/2010 - 00:21

谢谢超赣，终于能跑起来了，到了删除数据的这一步好像有点小问题。我应该注意些什么？还有这样的话，我可以继续往下做smooth应该没有问题吧。
Printing Graphics Windows to
C:\fMRI\restingstate\ProcessingDemoData\FunImg\spm_2010Jun21.ps
Saving Parameters..
Moving Normalized Files:Sub_001 OKMoving Normalized Files:Sub_002 OKMoving Normalized Files:Sub_003 OK
??? Error using ==> rmdir
C:\fMRI\restingstate\ProcessingDemoData\FunImg could not be removed.


Error in ==> DPARSF_run at 555
        rmdir('FunImg','s')

Error in ==> DPARSF>pushbuttonRun_Callback at 935
    [Error]=DPARSF_run(handles.Cfg);

Error in ==> gui_mainfcn at 96
        feval(varargin{:});

Error in ==> DPARSF at 39
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback
 

Submitted by YAN Chao-Gan on Thu, 06/24/2010 - 23:28

你打开了C:\fMRI\restingstate\ProcessingDemoData\FunImg里面的一个文件。
也许是用MATLAB，也许是MRIcroN打开的，导致DPARSF无法删除C:\fMRI\restingstate\ProcessingDemoData\FunImg
这个不删除后面做smooth也是没有影响的。