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Questions With This Site | Forum of resting-state fMRI

Questions With This Site

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  • Any questions you encountered with this site could be posted as a comment to this topic.
  • Please feel free to explore this researching site. I hope it be a start point of your resting-state fMRI research interest.

One advice is reading “How To Ask Questions The Smart Way”. And another advice may seem on the contrary: never hesitate to question yourself and then question in resting-state fMRI forum.

DPARSFA error

 I am new to the field of resting - state fMRI . I started my data analysis with  DPARSF Advanced version 2.2 and I wanted to calculate ALFF fALFF and Functional connectivity in MNI space with traditional Order. Then I selected from the Batch of DPARSFA "Calculate in MNI space: traditional order" and unchecked the boxes of "Remove first time points" and "Slice timing"  according to technical properties of the fMRI I use. Then at some points in MATLAB main is reported this error message and I could not carry on with my analysis.

Moving Head Motion Corrected Files:Sub_001 OK
Reorienting T1 Image Interactively for Sub_001: 
Reference to non-existent field 'ReorientMat'.
 
Error in DPARSFA_run (line 1030)
        mat=DPARSFA_spm_image_Parameters.ReorientMat;
 
Error in DPARSFA>pushbuttonRun_Callback (line 1601)
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in gui_mainfcn (line 96)
        feval(varargin{:});
 
Error in DPARSFA (line 33)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating uicontrol Callback
I also noticed that when I uncheck the boxes Reorient Fun and Reorient T1 and check Crop T1 rearranging the dicom files of T1Raw in nii in T1Img the analysis will run correctly and I obtain maps of FC ALFF and fALFF but I am worried that some methodological mistakes could occur in this way.

Could please anyone help me? 

 


Re: Questions With This Site

 我在使用dynamicBC这个工具尝试进行分析的时候,按照manual来的时候,只有第一种的voxel-wise的FC,使用默认MASK没有任何问题。其他的计算方法都会报错,比如进行dynamic EC的voxel-wise时候,使用默认MASK,以及自己用REST制作的灰质MASK时候,都会提示:
??? Index exceeds matrix dimensions.

 
Error in ==> DynamicBC_run at 203
            ROI_sig = data(index{1},:)';
 
Error in ==> DynamicBC>wgr_run_check at 1126
    DynamicBC_run(F)
 
??? Error while evaluating uicontrol Callback

或者
??? Undefined function or variable "pathstr".

 
Error in ==> DynamicBC_sliding_window_GC at 138
        pathstr_v = strrep(pathstr,save_info.save_dir,fullfile(save_info.save_dir,'GC_Variance',filesep));
 
Error in ==> DynamicBC_run at 265
                DynamicBC_sliding_window_GC(ROI_sig,slw_winsize,slw_overlapsize,pvalue,slw_order,save_info);
 
Error in ==> DynamicBC>wgr_run_check at 1126
    DynamicBC_run(F)
 
??? Error while evaluating uicontrol Callback
数据使用的是自己的静息数据,或者廖老师在西大讲课时候的示例数据,都会这样报错,其他全部按照manual来的,我估计是MASK的问题,请问这个MASK的制作应该是怎么弄的?
manual说是自己制作的灰质MASK,为什么我即使用默认MASK都会报错呢





 

Re: Questions With This Site

估计是mask大小不匹配,建议不用默认的mask,而是根据你数据的维度大小来选择mask。


Re: Questions With This Site

 非常感谢!我试了好多MASK,比如REST里的61x73x61MASK,或者其他软件做出来的灰质MASK,或者经过REST重采样的灰质MASK都是这种错误,,
我再试试,,谢谢老师!

Re: Questions With This Site

我的原始图像都是4dnii格式(在project 1000上下载),用spm的display查看,发现原点不在AC-PC上,用DPARSFA预处理-----配准结果不正确;后来手动进行reorient之后配准结果还可以;我试了一下不进行reorient时,spm配准结果还是可以的;我想请问为什么在spm上不用reorient,配准结果还可以,在DPARSFA上必须进行reorient吗?

Re: Questions With This Site

尊敬的各位老师:

真心感谢您们开发出这么好的软件,大大提高了相关研究的效率!我现在刚入门,发现DPARSF的时候特别兴奋。

最近我遇到了一个问题。期待老师的解惑。我在使用DPARSF 基本版求AAL90个脑区的time course的时候,在去完协变量之后查看图像,脑的形状已经几乎看不出来了,如下图。我前面的步骤做了

Normal
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7.8 磅
0
2

false
false
false

MicrosoftInternetExplorer4

去除前10个时间点、时间层校正、头动矫正、基于回声平面成像模板的空间标准化、去线性漂移、0.01Hz0.08Hz的低频滤波、去除协变量(头动信息,脑白质信号,脑脊液信号,全脑均值信号)。其中我不太明白为什么之前已经做了头动矫正,去协变量的时候还需要再去除头动信息。所以我不知道是不是因为我去除协变量时,选中了头动信息才导致图像有问题的?

祝好
谭各津


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Re: Questions With This Site

 这是正常的情况,继续做就好!

Re: Questions With This Site

Hi,
I am new to re fMRI field. My analysis is simple: to assess and compare functional connectivity in 4 patient groups using 18 predetermined ROIs.
I ran REST- Functional Connectivity toolbox and got 1.) Pearson's r between each two ROIs within each group (FCmap.txt), 2.) z-transformed correlations for the same as 1.)(zFCmap.txt), and 3.) ROIFCmap.txt by group; what does this say exactly?: the functional connectivity among the individual ROI and all other predetermined ROIs within an individual patient?
How do I assess the statistical significance of 1.) and 2.)?

Perhaps dumb questions but it would help me a lot to know exactly what I am doing,
Thank you,
Spagetka

Re: Questions With This Site

 you should use z transformed correlaiton coefficient to perfrorm group analysis, that is zFCmap.txt which is pairwise correlation between ROIs. 

Re: Questions With This Site

 Hi,
Thank you for creating the freindly interface resting state fMRI. 
I want to calculate the cluster size using Rest AlphaSim. One of the input parameters is the mask file of the brain. My mask file is with '.mat' extension and the program doesn't allow it. Is it possible that you could convert the file to acceptable one for the rest program?

Thank you,
Eli.

Re: Questions With This Site

 if your mask file in mat extension is indeed a brain with the same dimension as the REST template (i.e., matrix size is 61*73*61), you can use REST_WriteNiftiImage to write this mat file out into a nifti formated image file. 

The inputs for REST_WriteNiftiImage are:
REST_WriteNiftiImage(Data,Head,imageOUT)

1. Data: your mat file when you read it into matlab

2. Head: you can use [head data] = REST_ReadNiftiImage('one_of_the_image_file_you_want_mat_file_turns_to_be'); to get.

3. imageOUT: the path and name you want your new image file to be. 

Suppose if you had a different data dimension for your mat file from the common REST template file, you need to use REST ---> utilities --> image resampling to resample your generated image file to 61*73*61, 3*3*3 mm voxel size.

用DPARSF跑数据,总是出错,求帮助

 用DPARSF跑数据,总是出错:

Calculating Functional Connectivity by Seed based Correlation Anlyasis...
Read 3D EPI functional images: "H:\Beijing-Nature\Patients\1\FunImgNormalizedSmoothedDetrendedFilteredCovremoved\sub001".??? Out of memory. Type HELP MEMORY for your options.
 
Error in ==> repmat at 104
    B = A(subs{:});
 
Error in ==> rest_to4d at 107
                    AllVolume =repmat(squeeze(AllVolume(:,:,:,1)), [1,1,1, nVolumn]);
 
Error in ==> y_SCA at 57
    [AllVolume,VoxelSize,theImgFileList, Header] =rest_to4d(AllVolume);
 
Error in ==> DPARSF_run at 1329
        y_SCA([AutoDataProcessParameter.DataProcessDir,filesep,FunImgDir,filesep,AutoDataProcessParameter.SubjectID{i}],
        ...
 
Error in ==> DPARSF>pushbuttonRun_Callback at 996
    [Error]=DPARSF_run(handles.Cfg);
 
Error in ==> gui_mainfcn at 96
        feval(varargin{:});
 
Error in ==> DPARSF at 48
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback
 
>> 

Re: 用DPARSF跑数据,总是出错,求帮助

 显示你内存不足。需要加内存才行。

Re: 用DPARSF跑数据,总是出错,求帮助

 谢谢你的回复!
祝好!

Scrubbing Strategies

Dear DPARSF users and developers,

I have just started using this powerful toolbox and almost everything seems to be clearly explained and straightforward. I have only two questions.. Sorry, if they have already been asked - I didn't manage to find the answers on the forum.

I am currently running my analysis using DPARSF 2.3 (ADVANCED edition). In addition to ROI-based connectivity analysis, I'm planning to run Independent Component Analysis on *ARWSFB images using GIFT toolbox. I am not going to regress any nuisances, but will do scrubbing.

Here are my questions:
1. Which interpolation strategies would you generally recommend for ICA and/or ROI-based connectivity (Nearest Neighbor, Linear, Cubic Spline)?
2. What is the rationale behind removing 1 and 2 timepoints before and after "bad event", correspondingly, as recommended by default? Wouldn't we have a good control by removing just 1 and 1 instead?

Thank you very much in advance!
=======
Regards,
Alex

Regarding pre-processing of RS fMRI data

Hi all,

I am quite new to this field and now working on theanalysis of resting state data from healthy individuals.
I have tried using DPARSFA and I find it quite helpful.
Here are some questions regarding optimizing the pipe line.

  How to decide which bounding box to be specified for for Normalization? On what basis  is the default value chosen?

 What voxel size should be specified for Normalization?

What FWHM value should be set for smoothing? How is it  related  to the parameters set for Normalization?

Please help me..
Thanks in advance..
Sincerely,
Akhil

Re: Regarding pre-processing of RS fMRI data

 Bounding box: it will be OK if the bounding box is big enough to cover the entire brain.
Voxel size: usually a little bit smaller than the original sampling size. For example, original sampling size is 3.75*3.75*4 mm, the re-sampled size could be 3*3*3. 
Spatial smoothing: literature usually uses 4-8 mm. 

Re: Questions With This Site

Hi. I have a problem but it might be a Matlab problem. when I want to run slice viewer in rest it crashes in the moment of overlaying the reHo or the Alff results. When I Open REST I get the following message:

Warning: image_toolbox not valid
> In rest_sliceviewer>InitControls at 1053
  In rest_sliceviewer at 74
  In rest_sliceviewer at 38
  In rest at 153

I have added the Image_processing_Toolbox81_win64 to the patth but still not working. Any ideas?

Thanks!

Re: Questions With This Site

 Frist I feel so sorry that I did not response you timely .I suggest that you can try to use SPM to see whether the problem still exists.I think it may be better to consult the software R & D by Professor Yan Chaogang who will give you  informed answers

 

Re: Questions With This Site

I think his problem is the installation of imaging processing toolbox for MATLAB.
BTW, I am not a professor yet. :)

Re: Questions With This Site

Hi,

Seems the image processing toolbox is not working. Or please re-install it by providing a license?


多组数据处理的ICA分析

各位老师好,我采集了一些静息态数据,现在把这些数据配对分成了六组(3对),想用独立成份分析(GIFT)看他们的成分差异,能不能一次把六组的数据都处理了?因为如果分成六次处理,然后挑选成份统计分析的话,我觉得应该会主观误差太大了,而且可能会遗漏成份,有没有让他们成份对应,然后可以方便区分成份的方法。谢谢

可以而且应该一次把六组处理了。

可以而且应该一次把六组处理了。

如何设置被试呢?

谢谢老师!可是我六组的数据并不一样多?分成三对后,数目各不相同。这样在用GIFT处理的时候,我就不知道该怎么设置了,试着分成两组三个session的话也会报错。这样应该怎么设置?请老师指导下具体的设置。谢谢!再次感谢老师的回复!

可以把6组看成不同的被试,不用session的那个,就是不

可以把6组看成不同的被试,不用session的那个,就是不同的被试。结果做出来后你在一一分开即可。

Re: 可以把6组看成不同的被试,不用session的那个,就是不

我想问老师一一分开具体是怎么做的呀?因为gift是以sub为单位打包压缩的,是把他们解压缩后,找到想要的component后,再做成文件夹吗?我用spm做one-sample t-test,用全脑做mask,没有发现任何voxel,到底是为什么呢?

AlphaSim和FDR校正严格性谁更大?

各位老师:
做静息态数据统计分析的时候,是不是模板应该选择的尽量的小,这样在做AlphaSim的时候就能用更小的cluster size值做阈值?为什么我的结果用FDR校正的时候有阳性结果,而用AlphaSim校正后就基本没有结果了。是不是先验知识不足的情况下,AlphaSim校正更严格?如果我用一个比AlphaSim小的阈值做出了结果,能报出来吗?应该怎么报?
谢谢!
致敬!

AlphaSim和FDR校正

你好,我也对你提出的问题感兴趣,AlphaSim和FDR校正的原理不是一样的,所以结果用FDR校正的时候有阳性结果,而用AlphaSim校正后就基本没有结果了。FDR矫正在体素多的时候更严格,用一个比AlphaSim小的阈值做出了结果,只能说明他禁不起AlphaSim矫正,可能经不起噪音等的影响,结果的可靠性是存在疑问的,但是也不代表他没有意义。

Re

通常意义上的FDR校正是不考虑空间宽度的,而AlphaSim和Gaussian random field theory correction是需要考虑空间宽度的。
你看一下FDR校正之后的结果零散吗?

致谢,追问

谢谢严老师回复。FDR得到的结果并不零散,是不是如果结果包含的体素较少时,使用FDR比AlphaSAim能保留更多的激活区,另外,如果我校正时使用的cluster阈值比AlphaSim要求的阈值下,报告结果的时候应该说校正了吗?

Re

如果不零散,应该不会经不起AlphaSim校正呀。
cluster阈值比AlphaSim要求的阈值下??

是的

谢谢严老师。是的,因为我用的半高全宽比较大,需要的阈值比较大,得到的cluster比AlphaSim要求的要小。如果我使用比AlphaSim小的阈值,感觉结果还是挺好的,也能一定程度上解释。不知道这样行不行?报告的时候说校正的了吗?再次感谢严老师!

Re

你用FDR校正,也是可以接受的。

请高人指点如何查看rest slice view的结果?

小弟我试着做了统计,用rest slice view得出结果,但是看不懂结果,请高人指点下,非常感谢
# voxels structure(对于voxel structure,这个是否指16个相接的体素每个体素的部位?下表中如此分散,例如:左侧海马只有2个voxel BA34区就一个voxel,这些点有没有意义?)
16 --TOTAL # VOXELS--
3 Midbrain
3 Left Brainstem
2 Limbic Lobe
2 Hippocampus_L (aal)海马
2 ParaHippocampal_L (aal)左侧海马旁回前扣带回皮层
2 Parahippocampa Gyrus
2 Left Cerebrum
1 brodmann area 34前扣带回皮层
1 Gray Matter
----------------------
Cluster 4
Number of voxels: 32
Peak MNI coordinate: 45 48 -15
Peak MNI coordinate region: // undefined // undefined // undefined // undefined // undefined // Frontal_Mid_Orb_R (aal)
Peak intensity: 3.9619(例如这个peak点在右侧额中回眶面,而右额中回有18个体素,右额中回眶面、额下回眶面分别有16个# voxels structure 和 15个体素,在报告结果时是否需要都报出来,还是只报右侧额中回眶面?其他脑区如BA11区怎么办?)
32 --TOTAL # VOXELS--
24 Right Cerebrum
21 Frontal Lobe
18 Middle Frontal Gyrus
16 Frontal_Mid_Orb_R (aal)右侧额中回眶面
15 Frontal_Inf_Orb_R (aal)右侧额下回眶面
6 brodmann area 11 额眶区(眶回,直回和上额回前侧的一部分)
6 Gray Matter
5 White Matter

Voxel masking

 Hello, I have some Resting state fMRI data an I want mask the voxels and use aal.but I dont know how to do?

回复

你好,我英语太差,如果用中文的话,我非常乐意和你交流下fMRI。

有关AAL模板问题

如果我要知道AAL模板中某个具体区域(比如Thalamus)所有点的坐标,应该如何获得?

Parametric test with GCA output

Dear REST experts,

Thanks for your recent works, REST-GCA :)
I am trying to perform granger causality analysis using REST-GCA. I conducted both coefficient-based and residual-based GCA for controls group and patients group and got several outputs for each group. These outputs were finally transformed into Z-value. Now, I'd like to perform between-group comparison using parametric test (i.e., two sample t-test). However, I am not sure what output files I use to do this.
(1) Is it right that two outputs ("GCA_x2y_1" and "GCA_y2x_1", which are not z-transformed values) for coefficient-based GCA are used to perform between-group comparison?
(2) Is it right that four outputs ("GCA_x2y_Transformed", "GCA_y2x_Transformed", "ZGCA_x2y_Transformed", and "ZGCA_y2x_Transformed") for residual-based GCA are used to compare both groups?

Please comments.
Thank you in advance.

请问一下用Dparsf选了DICOM to Nifiti以后,出现这个错误,是不是与原数据文件有关呢?

我用的是matlab2009a的版本,原数据是用西门子设备采集的,它的文件是没有扩展名的
??? Undefined function or method 'spm' for input arguments of type 'char'.

Error in ==> DPARSF_run at 120
[SPMversion,c]=spm('Ver');

Error in ==> DPARSF>pushbuttonRun_Callback at 939
[Error]=DPARSF_run(handles.Cfg);

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

Error in ==> DPARSF at 41
gui_mainfcn(gui_State, varargin{:});

??? Error while evaluating uicontrol Callback
谢谢!

Re

没装SPM

好的,谢谢

好的,谢谢

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dawnsong

A scientific site similiar to this site

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