DPABI: a toolbox for Data Processing & Analysis for Brain Imaging

 
 
DPABI: a toolbox for Data Processing & Analysis for Brain Imaging
 
DPABI is a GNU/GPL* toolbox for Data Processing & Analysis of Brain Imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI). Please refer to The R-fMRI Course to know more about how to use this toolbox. Add with subfolders for DPABI in MATLAB's path setting and enter "dpabi" in the command window to enjoy this powerful toolbox.
 
 
New features of DPABI_V2.1_160415:
1. DPARSF V4.1_160415 released.
1.1. Fixed a bug in DPARSF Basic Edition. The bug is that the white matter signal is always removed in nuisance regression (only exist in the Basic Edition). Thanks to the report of Liviu Badea.
1.2. DPARSF Advanced Edition: Add an option of “Add mean back” for nuisance regression. The mean will be added back to the residual after nuisance regression. This is useful for circumstances of ICA or task-based analysis.
1.3. DPARSF Advanced Edition: Re-run with global signal regression (DPARSFA_RerunWithGSR). Fixed a bug when “Remove first X time points” was defined, the number of time points will be adjusted accordingly now. Thanks to the report of Hua-Sheng Liu.
1.4. DPARSF Advanced Edition: Add a slice timing batch mode for MultiBand data. Users could specify a text timing file for a given participant in SliceOrderInfo.tsv. Please see http://wiki.rfmri.org/SliceTiming for more details.
2. DPABI Results Organizer (under “The R-fMRI Maps Project”): also save the text version of ROI signals.
3. Dual Regression added (under Utilities). Define a map, then regress the map on the 4D data for a participant, thus get a time series. Variance-normalize the time series, and then regress on the 4D data, thus get the dual regression map.
4. DPABI Image Calculator (under “Utilities”). Syntax changed, now includes: g1.*To4D((i1>2.3),100) Make a mask (threshold at 2.3 on i1) and then apply to each image in group 1 (group 1 has 100 images).
5. Donsenbach 160 ROIs were merged into a single mask file (Dosenbach_Science_160ROIs_Radius5_Mask.nii).
6. Fixed a bug in y_GroupAnalysis_Image: CovVolume read error.
7. Add "MultiSelect" Mode when user selected "Add Image" for several GUIs.
8. DPABI Image Calculator (under Utilities): Fixed a bug when removing image or directory. Now, when you remove the item, the identifier will be re-ordered.
9. DPABI Viewer: Added a colorbar mode for DPABI_VIEW, when you add "+" or "-" flag at the end in "Add Overlay's Colorbar" entry, DPABI_VIEW will use full colormap to display the overlay.
 
 
New features of DPABI_V2.0_151201 (together with DPARSF_V4.0_151201):
1. Compatible with MATLAB 2014b and later versions.
2. Process the data both with and without global signal regression (GSR). Check “Nuisance regressors setting” -> “Both with & without GSR”. Alternatively, you can call DPARSFA_RerunWithGSR.m. E.g., DPARSFA_RerunWithGSR(DPARSFACfg.mat); where DPARSFACfg.mat stores the previous parameters without GSR.
3. The processing steps are affixed to Results directories. The R-fMRI calculation parameters are also written to the header of the result files.
4. V4 processing parameter template is added. No smoothing before R-fMRI measure calculation (except for VMHC). This is used for comparing across studies and accumulate processed data.
5. DPABI Statistical Analysis. Add multiple comparison test after ANOVA, e.g., 'tukey-kramer' or 'hsd', 'lsd', 'dunn-sidak', 'bonferroni’ or ‘scheffe' procedures.
6. DPABI_VIEW: compatible with BrainNet Viewer 1.5. 
7. Fixed a "File too small" bug when .hdr/.img files are used.
8. Fixed a bug in y_Standardize.m: error when multiple files are defined.
9. Fixed a bug in DPABI Image Calculator: error in standard deviation calculation along the 4th dimension.
10. Results Organizer module: with this module, the users could organize the intermediate files for future processing with DPABI. In addition, the results could be organized for future use, and to be accumulated for the future R-fMRI maps project.
 
 
New features of DPABI_V1.3_150710:
1. SPM12 Compatible.
2. DPARSF_V3.2_150710 released.
3. DPARSF for Rat data released.
The Rat module is based on a Rat T2 template generated by Dr. Adam J. Schwarz et al. Please cite this paper when appropriate: Schwarz, A.J., Danckaert, A., Reese, T., Gozzi, A., Paxinos, G., Watson, C., Merlo-Pich, E.V., Bifone, A., 2006. A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI. Neuroimage 32, 538-550. (A T1 template was included as well. It's generated by normalizing 50 rats (two scans at PND45 or PND60) to that T2 template and then averaging (by Dr. Chao-Gan Yan)).
A video for rat data processing is available at http://d.rnet.co/DPABI_RatDataProcessing_20150520.mp4.
4. Fixed a bug in generating Voxel Specific Head Motion: missing gmdmp.
5. Fixed a bug in Group Analysis: when CovVolume is not defined.
6. Fixed a bug when calling BrainNet Viewer in DPABI_VIEW.
7. Fixed a bug in Standardization: ‘/‘ is not defined in Windows.
8. Fixed a bug in Image Calculator: output will be split as the input files when calculating group images.
 
New features of DPABI_V1.2_141101:
1. DPARSF V3.1 Basic Edition: Fixed a bug of missing DPARSF_run.
2. DPARSF V3.1: Fixed a bug that can not find ROI templates.
3. DICOM Sorter: Fixed a bug - “Add All” button doesn’t work.
4. DPABI Viewer: Fixed a bug when execute GRF or AlphaSim correction.
5. DPABI ROI Signal Extractor: New module added to DPABI->Utilities.
6. y_AlphaSim: Modified by Katharina Wittfeld -- moved the masking step in the code and also inserted several smaller edits, please click here to see the bug post.
7. Test-Retest Reliability: Intraclass Correlation Coefficient (ICC). New module added to DPABI->Utilities. Three ICC algorithms are supported: ANOVA Model, ReML Model and Linear Mixed Models. The algorithms are based on Dr. Xi-Nian Zuo and his colleague’s work. Please cite Dr. Zuo’s work as detailed in each function.
 
New features of DPABI_V1.1_140827:
1. New modules in DPABI Utilities:
1.1. Multiple T1 Images Averager. If you have multiple T1 runs for each subject, this module will coregister them and make a mean T1 image to put to "T1Img" for following analyses.
1.2. T1 Image Defacer. If you want to openly sharing your data, or simply transfer your data to others, this module will remove the face of the T1 images for privacy concerns. This module coregister the MNI template (mni_icbm152_t1_tal_nlin_asym_09c.nii) and MNI face mask (mni_icbm152_t1_tal_nlin_asym_09c_face_mask.nii) to the individual T1 image, and then remove the face and put to "T1ImgDefaced".
2. Bugs Fixed.
2.1. DPABI Viewer: Cluster report doesn't work correctly after GRF correction. Thanks for Vincent's report!
3. DPABI now can check the latest version and pop up a notice.
 
 
DPABI includes the following components.
 
1.     DPARSF 3.0 Advanced Edition.
 
New features in DPARSF 3.0 Advanced Edition.
 
1.1.  Quality control. Integrated GUI for QCing the functional and structural images, users can give ratings and comments during the step of interactive reorientation.
 
1.2.  Automask generation. For checking EPI coverage and generating group mask, the automasks (as in AFNI) will be generated based on EPI images.
 
1.3.  Brain extraction (Skullstrip). This step can improve the coregistration between functional and structural images. Most registration issues of previous DPARSF versions can be solved by including this step. For Linux and Mac users: Need to install FSL. For Windows users: Thanks to Chris Rorden's compiled version of bet in MRIcroN, the modified version can work on NIfTI images directly.
 
1.4.  Nuisance Regression. 1) Masks can be generated based on segmentation or SPM apriori masks; 2) Methods can be mean or CompCor [Note: for CompCor, detrend (demean) and variance normalization will be applied before PCA, according to (Behzadi et al., 2007)]; 3) Global Signal can be extracted based on Automasks.
 
2.     DPARSF 3.0 Basic Edition.
 
2.1.  DPARSF Basic Edition now is using the engine of DPARSF Advanced Edition.
 
2.2.  Nuisance Regression (in MNI space) is placed before filtering, according to (Hallquist et al., 2013).
 
3.     DPARSF for Monkey data.
 
3.1.  The monkey module is based on Rhesus Macaque Atlases for functional and structural imaging studies generated by Wisconsin ADRC Imaging Core. Please cite their papers when appropriate: (McLaren et al., 2010; McLaren et al., 2009).
 
3.2.  Of note, the origin of monkey atlas is different from human MNI atlas. Please make sure the correct origins are set at the steps of "reorienting Fun*" and "reorienting T1*".
 
4.     Preprocessing for task fMRI.
 
Task fMRI data can be preprocessed via DPABI-DPARSF.
 
5.     VBM.
 
VBM analyses can be performed via DPABI-DPARSF.
 
6.     Quality Control.
 
6.1.  QC Raw T1 images.
 
6.2.  QC Raw functional images.
 
6.3.  QC normalization effects. 1) QC on the pictures for checking spatial normalization. 2) Dynamically checking normalized T1, gray matter and functional images.
 
6.4.  Thresholding QC scores and removing un-qualified subjects.
 
6.5.  Generating Group masks based on normalized Automasks of each subject.
 
6.6.  Thresholding EPI coverage.
 
6.7.  Head motion report.
 
6.8.  Thresholding head motion.
 
7.     Standardization. Perform the following standardization according to (Yan et al., 2013).
 
7.1.  Mean Regression
 
7.2.  Mean Regression & SD Division
 
7.3.  Mean Regression & Log SD Regression
 
7.4.  Z - Standardization
 
7.5.  Mean Division
 
7.6.  Mean Subtraction
 
7.7.  Median-IQR Standardization
 
7.8.  Rank
 
7.9.  Quantile Standardization
 
7.10.               Gaussian Fit
 
8.     Statistical Analysis.
Smoothness estimation based on the 4D residual is built in regression function – smoothness is written to the NIfTI headers automatically. For AlphaSim and GRF multiple comparison correction, only using smooth kernel applied in preprocessing is NOT sufficient, please use the estimated smoothness instead.
 
9.     Viewer.
The DPABI_VIEW is based on spm_orthviews, but powered with convenient functions. Please try it out!
 
10. Utilities.
Utilities including DICOM Sorter, Image Calculator and Image Reslicer.
 
Project Initiator: YAN Chao-Gan
 
 
 
References
Behzadi, Y., Restom, K., Liau, J., Liu, T.T., 2007. A component based noise correction method (CompCor) for BOLD and perfusion based fMRI. Neuroimage 37, 90-101.
Hallquist, M.N., Hwang, K., Luna, B., 2013. The nuisance of nuisance regression: spectral misspecification in a common approach to resting-state fMRI preprocessing reintroduces noise and obscures functional connectivity. Neuroimage 82, 208-225.
McLaren, D.G., Kosmatka, K.J., Kastman, E.K., Bendlin, B.B., Johnson, S.C., 2010. Rhesus macaque brain morphometry: a methodological comparison of voxel-wise approaches. Methods 50, 157-165.
McLaren, D.G., Kosmatka, K.J., Oakes, T.R., Kroenke, C.D., Kohama, S.G., Matochik, J.A., Ingram, D.K., Johnson, S.C., 2009. A population-average MRI-based atlas collection of the rhesus macaque. Neuroimage 45, 52-59.
Yan, C.G., Craddock, R.C., Zuo, X.N., Zang, Y.F., Milham, M.P., 2013. Standardizing the intrinsic brain: towards robust measurement of inter-individual variation in 1000 functional connectomes. Neuroimage 80, 246-262.
 
*Some codes from REST V1.0 and V1.1 that are not complying with GNU GPL have been re-written here to comply GNU GPL. Some GNU GPL functions of REST V1.2 ~ V1.8 have been modified to be integrated here under GNU GPL.

 

Old Versions: V1.0 V1.1 V1.2 V1.3 V2.0

Forums:

I have used the new version of DPARSFA in dpabi toolbox to preprocess rest fmri data, and found the order had changed from "Filter->Remove Covariates" to "Remove Covariates -> Filter". Is the latter order better? (or how about the old order?)

By the way, the network really very slow [http://d.rnet.co/Course_DPABI_Chinese_140807.mp4 ], online video will pause after few seconds. If I choose to save the video onto my harddisk, then it will stop at less than 10M (0.0)......,So, will there could be another download link? May dropbox be OK :)

Hi,

For the order, please refer to 2.2. Nuisance Regression (in MNI space) is placed before filtering, according to (Hallquist et al., 2013). Hallquist, M.N., Hwang, K., Luna, B., 2013. The nuisance of nuisance regression: spectral misspecification in a common approach to resting-state fMRI preprocessing reintroduces noise and obscures functional connectivity. Neuroimage 82, 208-225.

For the course, I think that was caused by too many connections to the course at the same time. This should be a bandwidth limitation. I sincerely hope all the R-fMRI nodes can pay some attention (e.g., click, :) ) to the Google Ads at the bottom of each R-fMRI webpage, thus we can use the compensation to enhance our bandwidth for RFMRI.ORG. At the current stage, I have uploaded it to youtube, please click here to visit it on youtube.

Thanks a lot!

Best,

Chao-Gan

 

Thank you for your help :)

Best Regards,

Hongsheng

In original paper--Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI,which comput ALFF in a process: Preprocess --> Bandpass Filter --> Fast Fourier Transform(get the power spectrum) --> calculate ALFF

It seems that in DPASFA3.0 comput the ALFF : Remove Covariance--> ALFF computation --> Bandpass filter (In DPASFA2.3, bandpass filter follwing the ALFF calculation too)

the data process setup is the screenshot in first comment. Is it right to compute ALFF?

OR, should I start from Dir "FunImgARWSD",and set up DPASFA like bellow?

Best Wish,

Hongsheng

Hi Hongsheng,

I believe this order is better "It seems that in DPASFA3.0 compute the ALFF : Remove Covariance--> ALFF computation --> Bandpass filter (In DPASFA2.3, bandpass filter following the ALFF calculation too)".

You don't need to do filter before ALFF. And you can not do filter before fALFF. I guess you want to remove nuisance signals before ALFF/fALFF, at least the head motion effects, right?

Please see Yan, C.G., Cheung, B., Kelly, C., Colcombe, S., Craddock, R.C., Di Martino, A., Li, Q., Zuo, X.N., Castellanos, F.X., Milham, M.P., 2013. A comprehensive assessment of regional variation in the impact of head micromovements on functional connectomics. Neuroimage 76, 183-201. for this order.

Best,

Chao-Gan

 

 

Thanks again :). I do want to remove nuirance siganals before comput ALFF/Reho.

Now I find myself have missed many good papers....

Best Wish,

Hongsheng

Hi! Dr.Yan!

I got some questions about the result files of DPABI

1. Does 'FunImgARCFWS' contrains final files after all of the process I choosen? So I can use them for funcitonal connectivity analysis?

2. Does 'T1ImgNewSegment' contains VBM results that can be directly analysised? To my knowledge, 'smwc*' file are the results of VBM. However, I do not know 8mm,10mm or 12 mm Kernel Smoother was used in this file.

     In addition, what is the meaning of number '1,2,3' in their name? Gray matter, white matter and CSF?

Best Wish

Wei Liu

Hi Wei,

1. Yes, Yes.

2. Yes. 8mm, as you can see in the command window during the processing.

3. Yes.

Best,

Chao-Gan

Hi Chao-Gan,

Is there a new preferred citation for dpabi, or is the older one (2010) your preference?

Best,
Matt

Thanks, Matt!

We are trying to write one manuscript on DPABI. However, at the current stage, please cite the older one (2010).

Best,

Chao-Gan

 

Hi Chao-Gan,

For nonstandardized data, I've always been able to examine pairwise ROI connectivity by looking at the *.mat files in FumImgRCWSF_ROISignals.  What is the easiest way to do that for standardized data, given that there is no new FunImgRCWSF_ROISignals directory when you do the standardization?

Thanks,

Matt

Hi Matt,

I am not sure if I unerstand your question correctly. Here standardization you mean mean regression etc.?

For pair-wise FC, you can use GCOR (Saad, Z., Reynolds, R. C., Jo, H. J., Gotts, S. J., Chen, G., Martin, A., et al. (2013). Correcting brain-wide correlation differences in resting-state fMRI. Brain Connect. 3, 339–352.) or say  Whole brain mean iFC (Yan, C.G., Craddock, R.C., He, Y., Milham, M.P., 2013. Addressing head motion dependencies for small-world topologies in functional connectomics. Front Hum Neurosci 7, 910.) to regress out from the pair-wise FC.

Best,

Chao-Gan






Yes, I mean what you wrote about in your 2013 paper (so mean + ln(stdev)).  The standardization module gives new zROI?FMAP_*.nii files, but not new ROICorrelation_FisherZ_*.mat
files.  But I guess I can use GCOR, as you say.

 

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On Behalf Of The R-fMRI Network
Sent: Friday, February 06, 2015 5:06 PM

To: rfmri.org@rnet.co

Subject: Re: [RFMRI] DPABI: a toolbox for Data Processing & Analysis of Brain Imaging

 

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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Matt,

I am not sure if I unerstand your question correctly. Here standardization you mean mean regression etc.?

For pair-wise FC, you can use GCOR (Saad, Z., Reynolds, R. C., Jo, H. J., Gotts, S. J., Chen, G., Martin, A., et al. (2013). Correcting brain-wide correlation differences in resting-state fMRI. Brain Connect. 3, 339–352.) or say  Whole brain mean iFC (Yan,
C.G., Craddock, R.C., He, Y., Milham, M.P., 2013. Addressing head motion dependencies for small-world topologies in functional connectomics. Front Hum Neurosci 7, 910.) to regress out from the pair-wise FC.

Best,

Chao-Gan



Online version of this post:
http://rfmri.org/comment/3506#comment-3506

 

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Hello,

I get this error using DPARSFA:  

Error using y_alff_falff (line 122)
Subscripted assignment dimension mismatch.
 
Error in DPARSFA_run>(parfor body) (line 3414)
            [ALFFBrain, fALFFBrain, Header] =
            y_alff_falff([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName,filesep,AutoDataP
            Error in DPARSFA_run (line 3404)
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in DPARSFA>pushbuttonRun_Callback (line 1670)
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in gui_mainfcn (line 96)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
Caused by:
    Subscripted assignment dimension mismatch.
 
Error while evaluating uicontrol Callback
 
The mask gets the suffix "91x109x91", but I checked the actual dimensions and they were "61x73x61".

I tried again replacing 61x73x61 for 91x109x91 in the DPARSFA_run.mat script, but it still doesn't work.

I'd really appreciate any suggestion about how to solve this problem.

Thanks in advance,

mireia

 

Hi Mireia,
What's the resolution of your functional images? Could you post a snapshot of your settings here?

Best,

Chao-Gan


Hi Chao-Gan,

Here I paste the info. Please, let me know if you need to know anything else.

Thanks,

mireia

Funcional image without normalization (folder FunImg)

 

Funcional 4D image with normalization (folder FunImgARCWS)

 

Mask --> AllResampled_BrainMask_05_91x109x91.nii (folder mask)

 

Hi mireia,

I can not see the figures you posted. Please post using the "image" button on the tools line.

I guess you are calculating ALFF for images without normalization? Then you should not use AllResampled_BrainMask_05_91x109x91.nii. In such a case, choose the default setting for "Calculate in Original Space".

Best,

Chao-Gan

Hi Chao-Gan,
I had trouble pasting the images in the forum. So, I attach the info about the ressolution of the functional images in a Word file here.

Brw, I do normalize data. 

As a reminder of the error I get:
Error using y_alff_falff (line 122)
Subscripted assignment dimension mismatch.

Error in DPARSFA_run>(parfor body) (line 3414)
            [ALFFBrain, fALFFBrain, Header] =
            y_alff_falff([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName,filesep,AutoDataP
            Error in DPARSFA_run (line 3404)
        parfor i=1:AutoDataProcessParameter.SubjectNum

Error in DPARSFA>pushbuttonRun_Callback (line 1670)
    [Error]=DPARSFA_run(handles.Cfg);

Error in gui_mainfcn (line 96)
        feval(varargin{:});

Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});

Caused by:
    Subscripted assignment dimension mismatch.
 
Error while evaluating uicontrol Callback

The mask gets the suffix "91x109x91", but I checked the actual dimensions and they were "61x73x61".

I tried again replacing 61x73x61 for 91x109x91 in the DPARSFA_run.mat script, but it still doesn't work.


Thank you!

mireia






On Tue, Feb 17, 2015 at 4:34 PM, The

Hi Dear Developers,

Thanks for the great work! Could you please refresh the download link, as it does not seem to work.

===

Regards,

Alex

Dear Alex,

Thank you very much for your report!

The problem has been fixed. Please go ahead to download it. (As we are collecting feedback from the users, please kindly spend 2 minutes to finish a very brief survey, thanks!)

Please let us know if you encounter any problems or get any bugs.

Best,

Chao-Gan

 

Hello 

 

I posted this to the mailing list :

 

"Dear Yan,

 
I did download now the demo but still it does not recognise it. I re-arranged my files as into a folder called 
FunImg/Sub_001/S1.nii
FunImg/Sub_002/S2.nii
 
But still as well when I point to the directory the white box under the directory where it says participants is empty.
 
Can you please help?
 
Thanks
 

Note pleas that I tried also the demo and watched the videos and organized the data ( NIFITI) in the same ibstructed way. The demo was not recognized as well. i cannot see the folders of the subjects.

can you please help by providing at least an example of what to do?

Hi Aser,
 

Please spend some time to http://rfmri.org/course for how to use the software.
 

If you are using the demo data, you need to keep the FunRaw and T1Raw structure. And set the starting directory at the bottom right.

 
Best,
 
Chao-Gan

 

Hi all,

 

I got this error message and I am not sure why and where to solve it.  See below please:

 

Also Do I have once this is fixed to repat the whole process again ?

 

/bin/bash: bet: command not found

/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
/bin/bash: bet: command not found
Bet finished
Copying T1 image Files:Sub_003 OKCopying T1 image Files:Sub_002 OKCopying T1 image Files:Sub_001 OKCopying T1 image Files:Sub_009 OK
Copying T1 image Files:Sub_006 OKCopying T1 image Files:Sub_005 OKCopying T1 image Files:Sub_004 OKCopying T1 image Files:Sub_008 OKCopying T1 image Files:Sub_007 OK
 
Error using DPARSFA_run>(parfor body) (line 1608)
Index exceeds matrix dimensions.
 
Error in DPARSFA_run (line 1551)
    parfor i=1:AutoDataProcessParameter.SubjectNum
 
 
Error in DPARSF_run (line 113)
[Error] = DPARSFA_run(Cfg);
 
 
Error in DPARSF>pushbuttonRun_Callback (line 1122)
    [Error]=DPARSF_run(handles.Cfg);
 
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});

严老师:

您好!

我现在匹兹堡医学院的一个实验室做核磁的一些数据分析,但在这里我的电脑上不能用Matlab,必须通过Putty和VNC连接到主机上使用。 然而这种远程连接十分麻烦,一用DPABI就报错,请您帮忙看看。

十分感谢!

Warning: File: DPARSFA_run.m Line: 673 Column: 66
The temporary variable SliceOrder will be cleared at the
beginning of each iteration of the parfor loop.
Any value assigned to it before the loop will be lost.  If
SliceOrder is used before it is assigned in the parfor loop, a
runtime error will occur.
See Parallel for Loops in MATLAB, "Temporary Variables". 
> In DPARSF_run at 113
  In DPARSF>pushbuttonRun_Callback at 1122
  In gui_mainfcn at 96
  In DPARSF at 51 
Warning: File: DPARSFA_run.m Line: 928 Column: 83
The temporary variable RefFile will be cleared at the
beginning of each iteration of the parfor loop.
Any value assigned to it before the loop will be lost.  If
RefFile is used before it is assigned in the parfor loop, a
runtime error will occur.
See Parallel for Loops in MATLAB, "Temporary Variables". 
> In DPARSF_run at 113
  In DPARSF>pushbuttonRun_Callback at 1122
  In gui_mainfcn at 96
  In DPARSF at 51 
Warning: File: DPARSFA_run.m Line: 2632 Column: 24
The temporary variable DirImg will be cleared at the beginning
of each iteration of the parfor loop.
Any value assigned to it before the loop will be lost.  If
DirImg is used before it is assigned in the parfor loop, a
runtime error will occur.
See Parallel for Loops in MATLAB, "Temporary Variables". 
> In DPARSF_run at 113
  In DPARSF>pushbuttonRun_Callback at 1122
  In gui_mainfcn at 96
  In DPARSF at 51 
Warning: File: DPARSFA_run.m Line: 4201 Column: 32
The temporary variable DirImg will be cleared at the beginning
of each iteration of the parfor loop.
Any value assigned to it before the loop will be lost.  If
DirImg is used before it is assigned in the parfor loop, a
runtime error will occur.
See Parallel for Loops in MATLAB, "Temporary Variables". 
> In DPARSF_run at 113
  In DPARSF>pushbuttonRun_Callback at 1122
  In gui_mainfcn at 96
  In DPARSF at 51 


Error using cd
Cannot CD to /data/home/qiuh/data/Analysis/FunImg (Name is
nonexistent or not a directory).

Error in DPARSFA_run (line 542)
        cd([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName]);
        
Error in DPARSF_run (line 113)
[Error] = DPARSFA_run(Cfg);

Error in DPARSF>pushbuttonRun_Callback (line 1122)
    [Error]=DPARSF_run(handles.Cfg);

Error in gui_mainfcn (line 96)
        feval(varargin{:});

Error in DPARSF (line 51)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating uicontrol Callback

Error using load
Argument must contain a string.

Error in DPARSF>pushbuttonLoad_Callback (line 1057)
    load([pathname,filename]);

Error in gui_mainfcn (line 96)
        feval(varargin{:});

Error in DPARSF (line 51)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating uicontrol Callback

>> 

你好!

Error using cd
Cannot CD to /data/home/qiuh/data/Analysis/FunImg (Name is
nonexistent or not a directory).

看起来是数据整理的问题。你的处理参数是什么样子的呢?

祝一切顺利!

超赣

我只是用了6个人做练习,这些数据都是以前用dparsf跑出来过的啊。只是这次用的是被试自己的T1像做配准,其他没有什么特别的。 有没有可能是主机不让我读取或者储存数据呢?

还有前面那部分报错是什么意思呢?

非常感谢严老师!

严老师:

您好!

我找这边的技术人员看了一下,好像当使用VNC 连接的情况下,Dpabi 是不能正常运行,后来改为用MobaXterm 就好多了。

现在我跑数据又出现以下报错,请问下一这是怎么回事,需如何处理?

Error using file_array/subsref>subfun (line 80)

An UndefinedFunction error was thrown on the workers for 'file2mat'.  This

might be because the file containing 'file2mat' is not accessible on the

workers.  Use addAttachedFiles(pool, files) to specify the required files to

be attached.  See the documentation for 'parallel.Pool/addAttachedFiles' for

more details.

 

Error in file_array/subsref (line 60)

    t = subfun(sobj,args{:});

 

Error in nifti/subsref>rec (line 219)

            t = subsref(t,subs(2:end));

 

Error in nifti/subsref (line 45)

varargout = rec(opt,subs);

 

Error in DPARSFA_run>(parfor body) (line 575)

                    y_Write(Nii.dat(:,:,:,AutoDataProcessParameter.RemoveFirstTimePoints+1:end),Nii,DirImg(1).name);

                   

Error in DPARSFA_run (line 543)

        parfor i=1:AutoDataProcessParameter.SubjectNum

 

Error in DPARSF_run (line 113)

[Error] = DPARSFA_run(Cfg);

 

Error in DPARSF>pushbuttonRun_Callback (line 1122)

    [Error]=DPARSF_run(handles.Cfg);

 

Error in gui_mainfcn (line 96)

        feval(varargin{:});

 

Error in DPARSF (line 51)

    gui_mainfcn(gui_State, varargin{:});

 

Caused by:

    Undefined function 'file2mat' for input arguments of type 'struct'.

 

Error while evaluating uicontrol Callback

非常感谢!

邱海棠

通常这个错误是因为你的spm8没有安装update包或者你的matlab的搜索路径中
有REST1.8,REST1.8内置了一部分spm5的命令,所以可能matlab在搜索时候会使用
REST中的spm函数,导致版本不兼容而报错,可以在使用DPABI的时候把REST从工作
路径中移除。
祝好,
鑫迪
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]
On Mon, Nov 30, 2015 at 04:11:27PM +0000, The R-fMRI Network wrote:

Commented by 邱海棠 (echoqiu77)

鑫迪,

您好!

谢谢您的回复,问题得到完美解决,我的数据已经能够畅快地运行,真是太好了!

我现在尝试用DPABI 处理nii格式的文件,因为这边实验室对这个软件不熟悉,希望我先用他们跑过的数据再跑一下看看结果如何,所以我只能按照他们的要求来跑。我也很希望能够得到不错的结果,这样我以后的工作可以轻松很多,也可以给他们介绍这个强大又方便的软件。

他们让我略过slice timing这一步,所以我在basic dparsf里就没有勾选从DICOM 转成NII 这一步,也没有勾选slice timing,结果报错如下:麻烦您帮我看下又是哪里出了问题, 非常感谢!

Error using DPARSFA_run>(parfor body) (line 544)

Cannot CD to /data/home/qiuh/data/Analysis/FunRaw/CU0009_1R1_bold_resting2.nii

(Directory permission denied).%%%是因为nii格式的文件不能直接读取的意思吗?

 

Error in DPARSFA_run (line 543)

        parfor i=1:AutoDataProcessParameter.SubjectNum

 

Error in DPARSF_run (line 113)

[Error] = DPARSFA_run(Cfg);

 

Error in DPARSF>pushbuttonRun_Callback (line 1122)

    [Error]=DPARSF_run(handles.Cfg);

 

Error in gui_mainfcn (line 96)

        feval(varargin{:});

 

Error in DPARSF (line 51)

    gui_mainfcn(gui_State, varargin{:});

 

Caused by:

    Error using cd

    Cannot CD to /data/home/qiuh/data/Analysis/FunRaw/CU0009_1R1_bold_resting2.nii

    (Directory permission denied).

 

Error while evaluating uicontrol Callback

另外还想问一个问题,我在跑另一组数据进行中没有问题,但是我是用被试自己的T1象进行配准的,那么当出来图像,调整选项里有一个up 我不知道是调节哪个方向的?

非常感谢!

这个看起来是该路径权限错误,具体得问超赣了,我并没有遇到过这个情况。
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this l

看起来你这个问题是关于数据整理的。建议再过一遍http://rfmri.org/course#RfMRICourseV2_zh
超赣


On Thu, Dec 3, 2015 at 6:20 PM, The R-fMRI Network <

hello YAN please i have this error

 Extracting ROI signals finished, elapsed time: 21.0938 seconds.
You do not have sufficient privilege to perform this operation. 
 
Extracting ROI signals...??? Error using ==> y_ReadAll at 60
The input name is not supported by y_ReadAll:
F:\aa\ProcessingDemoData\FunImgARglobal\Sub_003
 
Error in ==> y_ExtractROISignal at 56
    [AllVolume,VoxelSize,theImgFileList, Header]
    =y_ReadAll(AllVolume);
 
Error in ==> DPARSFA_run>(parfor body) at 2598
                y_ExtractROISignal([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName,filesep,AutoDataProcessParameter.SubjectI
                Error in ==> parallel_function at 473
            F(base, limit);
 
Error in ==> DPARSFA_run at 2453
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in ==> DPARSFA_RerunWithGSR at 87
[Error]=DPARSFA_run(Cfg);
 
Error in ==> DPARSFA>pushbuttonRun_Callback at 1764
        [Error]=DPARSFA_RerunWithGSR(handles.Cfg);
 
Error in ==> gui_mainfcn at 96
        feval(varargin{:});
 
Error in ==> DPARSFA at 30
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback
 
 

 Dear YAN i have this error
I checked the FunImgARglobal\Sub_003 there is no file
Extracting ROI signals finished, elapsed time: 14.1406 seconds.
You do not have sufficient privilege to perform this operation. 
 
Extracting ROI signals...??? Error using ==> y_ReadAll at 60
The input name is not supported by y_ReadAll: F:\bb\ProcessingDemoData\FunImgARglobal\Sub_003
 
Error in ==> y_ExtractROISignal at 56
    [AllVolume,VoxelSize,theImgFileList, Header] =y_ReadAll(AllVolume);
 
Error in ==> DPARSFA_run>(parfor body) at 2598
                y_ExtractROISignal([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName,filesep,AutoDataProcessParameter.SubjectI
                Error in ==> parallel_function at 473
            F(base, limit);
 
Error in ==> DPARSFA_run at 2453
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in ==> DPARSFA_RerunWithGSR at 87
[Error]=DPARSFA_run(Cfg);
 
Error in ==> DPARSFA>pushbuttonRun_Callback at 1764
        [Error]=DPARSFA_RerunWithGSR(handles.Cfg);
 
Error in ==> gui_mainfcn at 96
        feval(varargin{:});
 
Error in ==> DPARSFA at 30
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback

Hi,

I guess the symbolic link of FunImgARglobal is not successfully created.

You can simply copy FunImgAR to FunImgARglobal to fix this problem.

Best,

Chao-Gan

Thanks alot Yan

Hi everyone, a basic question: Are the processed images in folder FunImgARWSDFC in the MNI space? I believe this is the case but wish to double check. Thanks!

Hi,
Yes. W means normalized into MNI space.

Best,

Chao-Gan







Thank you, Chao-Gan.

On 2/27/16 20:20, The R-fMRI Network
wrote:
type="cite">

[To post a comment, please reply to
rfmri.org@gmail.com ABOVE this line]


Commented by YAN Chao-Gan (YAN
Chao-Gan)

Hi,

Yes. W means normalized into MNI space.

Best,

Chao-Gan

Good evening,

I have used the EPI template for the normalization of resting-state data in DPARSF. However, I am wondering whether there is any way that I could take a look at the EPI template which is then generated by DPARSF over all subjects. With the DPARSF-Viewer I can only find the individual normalized brains.

With kind regards,

Markus Loose

if SPM12, SPMPath/OldNorm/EPI.nii

Best,

Thank you very much for the response :-)
I have another question:
Is it possible in DPARSF to resample the voxel size at any point, preferably before the motion correction?

With kind regards

Markus Loose

Hi Markus,

You can try DPABI->Utilities->Image Reslicer.

Best,

Chao-Gan

Hello,

My matlab reported the following error, while using dpabi's paired t test tool. Really need help. Thank you!

My matlab version is: R2012b; the package of: rest version: REST_V1.8_130615; spm 12, have been setpath.

The error was reported as: 

______________________________________________
Reading images from "I:\XXX.nii" etc.
Undefined function 'file2mat' for input arguments of type 'struct'.
 
Error in file_array/subsref>subfun (line 80)
t = file2mat(sobj,varargin{:});
 
Error in file_array/subsref (line 60)
    t = subfun(sobj,args{:});
 
Error in file_array/numeric (line 13)
out = subsref(fa,struct('type','()','subs',{vo}));
 
Error in file_array/double (line 11)
out = double(numeric(fa));
 
Error in y_Read (line 71)
    Data = double(Nii.dat);
 
Error in y_ReadRPI (line 41)
[Data,Header] = y_Read(FileName,VolumeIndex);
 
Error in y_ReadAll (line 70)
    [Data, VoxelSize, Header] = y_ReadRPI(FileList{1});
 
Error in y_TTestPaired_Image (line 29)
    [AllVolume,VoxelSize,theImgFileList, Header] = y_ReadAll(DependentDirs{i});
 
Error in DPABI_STAT_TOOL>ComputeButton_Callback (line 500)
        y_TTestPaired_Image(S, OutputName, MaskFile, ImageCell, TextCell);
 
Error in gui_mainfcn (line 96)
        feval(varargin{:});
 
Error in DPABI_STAT_TOOL (line 42)
    gui_mainfcn(gui_State, varargin{:});
 
Error in
@(hObject,eventdata)DPABI_STAT_TOOL('ComputeButton_Callback',hObject,eventdata,guidata(hObject))
 
 
Error while evaluating uicontrol Callback
________________________________________________________
I have tried the one/two sample t test, the same error occurred every time.
 
Thank you!
Best,
Qing
>> 

I have asked some friends and fixed the problem.

I re- setpathed the spm package and the statistical tools worked again.

thank you.

Best,

Qing