Frequently Asked Questions (FAQ)

Submitted by YAN Chao-Gan on
Hi all,
 
Besides the information provided in the Courses, there were still lots of questions about resting-state fMRI data processing. Here we'd like to build a FAQ section for your convenience. However, the FAQ is just started and will be developed gradually.
 
Best,
 
Chao-Gan
 
1. What are the toolboxes needed for DPABI/DPARSF?
A: DPABI/DPARSF works well with MATLAB and Statistics and Machine Learning Toolbox, Image Processing Toolbox and Signal Processing Toolbox. In addition, Parallel Computing Toolbox is needed if the users want to process multiple subjects in parallel computing mode.
 
2. How to solve the problem of “out of memory”?
A: Please refer to http://rfmri.org/OutOfMemory
 
3. What’s the ROI information of the templates provided in DPARSF?
 
4. Why the data after nuisance regression looks so strange (distorted)?
 
5. How to compare a single case with a group of controls?
 
6. Does the part "Reorienting T1 Image Interactively for XXX" require any input from the user?
 
7. What’s the input for smoothness estimation?
 
8. What’s the option of “IsTwoTailed” in GRF correction?

9. How to convert from voxel index to MNI coordinates and vice versa?
A: Please refer to http://www.rfmri.org/node/1300
 
10. Why linear trend should be removed before filtering?
A: Please refer to http://www.rfmri.org/node/1515
 
11. Why "calling other os commands from MATLAB" choke the processing, e.g., dcm2nii?
A: Please refer to http://www.rfmri.org/comment/2979#comment-2979
 
12. How to solve: Error using gifti/save Too many input arguments?

老师您好：

我是在做TFCE矫正的过程中出现了以下的报错，

错误使用 palm_takeargs (line 1133)

Unknown option: "Z:\data\rest\Hippocampus_FC\dpabi_analysis\349r\TFCE\Temp\Design.csv"

出错 palm_core (line 33)

[opts,plm] = palm_takeargs(varargin{:});

出错 palm (line 81)

palm_core(varargin{:});

出错 y_GroupAnalysis_PermutationTest_Image (line 102)

palm([TempDir,filesep,'PALMConfig.txt']);

出错 y_Correlation_Image (line 74)

    y_GroupAnalysis_PermutationTest_Image(DependentVolume,Regressors,OutputName,MaskFile,CovariateVolume,Contrast,'T',0,Header,PALMSettings);

    出错 DPABI_STAT_TOOL>ComputeButton_Callback (line 536)

        y_Correlation_Image(S, SeedSeries, OutputName, MaskFile, ImageCell, TextCell, PALMSettings);

出错 gui_mainfcn (line 95)

        feval(varargin{:});

出错 DPABI_STAT_TOOL (line 42)

    gui_mainfcn(gui_State, varargin{:});

出错 @(hObject,eventdata)DPABI_STAT_TOOL('ComputeButton_Callback',hObject,eventdata,guidata(hObject))

 

 

Error while evaluating uicontrol Callback

我的DPABI版本是3.1，matlab2014a，想请教一下这种报错一般是什么原因，需要怎么处理？谢谢您的回复。

<div>Chris Rorden's dcm2niiX version v1.0.20200331 &nbsp;(JP2:OpenJPEG) (JP-LS:CharLS) MSC1900 (64-bit Windows)&nbsp;</div><div>Warning: only processing last of 3 input files (recompile with 'myEnableMultipleInputs' to recursively process multiple files)&nbsp;</div><div>Error: Input folder invalid: stimulation\FunRaw\Sub_045\GUO_QINGQING.MR.SUS_HEAD.0011.0001.2020.09.14.15.09.58.997810.96394369.IMA&nbsp;</div><div>Converting Functional Images:Sub_045 OK</div><div>&nbsp;</div><div>严老师您好！我想请教下您，我为什么用dipabi 在第一步就报错 ，dicom 文件没法转成nifti 文件 FunImg文件夹为空，请指点！</div>

严老师您好，我做了三组数据的ANCOVA，然后用hsd做多重校正，得到的三组之间的对比，其中G1VSG2 G1VSG3，两个结果不能在VIEWER中显示，但是G2VSG3却可以正常显示，报错信息如下：

错误使用 repmat
复制因子必须为整数行矢量或整数标量。
 
出错 y_AdjustColorMap (line 74)
    NewColorMap(Begin:End,:) = repmat(OriginalColorMap(iColor,:),[Segment 1]);
 
出错 w_OverlayList>RedrawOverlay (line 1354)
ColorMap = y_AdjustColorMap(ColorMap,...
 
出错 w_OverlayList>Accept_Callback (line 1423)
            OverlayHeader=RedrawOverlay(OverlayHeader, handles.MainFig);
 
出错 gui_mainfcn (line 95)
        feval(varargin{:});
 
出错 w_OverlayList (line 42)
    gui_mainfcn(gui_State, varargin{:});
 
出错 @(hObject,eventdata)w_OverlayList('Accept_Callback',hObject,eventdata,guidata(hObject))
 
 
错误使用 waitfor
Error while evaluating UIControl Callback
请问这是什么原因，要怎么解决？
谢谢！

严老师您好：

         关于repeated measures ANCOVA在dpabi软件统计模块的使用中和ANCOVA有什么区别吗？例如只有一组病人治疗前后两个时间点的数据可以用repeated measures ANCOVA吗？我在使用这个模块时将两个时间点影像数据放进去可以出结果，但它这个和配对t检验有什么区别吗？

           感谢老师    

 

 

chenyuxinxin

Sun, 11/28/2021 - 05:39

Permalink

老师好，在linux系统下运行dparsf时遇到这样的情况，不知道哪里的问题？
在windows运行没有出现过。谢谢老师解答
 
Generating the pictures for checking normalization: Sub_001 OK. 没有为类 'matlab.ui.Figure' 的值定义函数 'subsindex'。
 
出错 y_spm_orthviews>addcolourbar (line 883)
if st{curfig}.mode == 0,
 
出错 y_spm_orthviews>addtruecolourimage (line 824)
addcolourbar(1,bset);
 
出错 y_spm_orthviews (line 511)
        addtruecolourimage(varargin{1}, varargin{2},varargin{3}, varargin{4}, ...
 
出错 y_Call_spm_orthviews (line 149)
    y_spm_orthviews('Addtruecolourimage',H,BrainHeader,ColorMap,1-Transparency,PMax,NMax);
 
出错 DPARSFA_run (line 3222)
            H = y_Call_spm_orthviews(Ch2Filename,0,0,0,18,Filename,jet(64),0,250,H,0.8);
 
出错 DPARSFA_RerunWithGSR (line 100)
[Error]=DPARSFA_run(Cfg);
 
出错 DPARSFA>pushbuttonRun_Callback (line 1851)
        [Error]=DPARSFA_RerunWithGSR(handles.Cfg); %YAN Chao-Gan, 210419. In case the subject ID was changed during the first run,
        e.g., thresholding quality after reorient.%[Error]=DPARSFA_RerunWithGSR(handles.Cfg);
 
出错 gui_mainfcn (line 95)
        feval(varargin{:});
 
出错 DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
计算 UIControl Callback 时出错。

严老师您好，我在对图像进行FirldMap Correction之后，图像被拉长，形状变得很奇怪，导致后面的配准效果很差，不知道这是什么原因导致的呢？以下是校正前后的影像，以及vdm5_scfpm_sc*.nii的图像：

Dear Dr Yan:

  Hello!
  I wanna search for help about how to adjust the order of preprocessing when preprocessing in Dpabi, for example, some projects may do Slice Timing first and then Realign, and some projects may do Realign first and then Slice Timing, and I don't see how to adjust the order of preprocessing in Dpabi, so consult you!
  I wish you success in your work, happiness in your family and all the best! God bless you！
Sincerely,
Jial

YAN Chao-Gan

Thu, 08/10/2023 - 01:12

Permalink

Hi Jial,

 

A simple way is to run single step for realign, starting directory name with FunImg. And then run a single step of slice timing, starting directory name with FunImgR. Then you will have FunImgRA.

 

您好，现在使用DPABI的时候，在matlab中输入dpabi不会出现之前的ui界面，会一直卡住在如下界面，之前使用都没问题，是最近才出现的。但是输入DPARSF还是可以出现ui界面的不知道是为什么，希望可以得到解答。

严老师您好！

        在使用DPARSF5.4进行rest-fMRI预处理时normalize voxel size设置为[2 2 2]（原始数据采集voxelsize=3.75，但由于fmriprep-voxelsize默认为2且很多template-voxelsize为2，所以还是设置为2进行预处理），其他参数未变，结果PicturesForChkNormalization文件夹里面所有被试的图都如下所示，但最后生成的预处理完后的.nii文件没有异常，且整个预处理过程没有报错，请问这一步标化是否存在问题？最后生成的.nii文件是否可以用于后续分析呢？

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