Data Processing Assistant for Resting-State fMRI (DPARSF)

Submitted by YAN Chao-Gan on

 
 
Data Processing Assistant for Resting-State fMRI (DPARSF)
 
 
Data Processing Assistant for Resting-State fMRI (DPARSF) is a convenient plug-in software within DPABI, which is based on SPM. You just need to arrange your DICOM files, and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data, functional connectivity, ReHo, ALFF/fALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. You can use DPARSF to extract ROI time courses efficiently if you want to perform small-world analysis. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient your images interactively or define regions of interest interactively. You can skip or combine the processing steps in DPARSF advanced edition freely. Please download a MULTIMEDIA COURSE to know more about how to use this software. As a component of DPABI, please add with subfolders for DPABI in MATLAB's path setting and enter "dpabi" in the command window to enjoy this powerful toolbox.
 
The latest release is DPARSF_V5.3_210101. Please download DPABI to enjoy it!  
 
New features of DPARSF_V5.3_220101  (download at http://rfmri.org/dpabi)
1. Use 3dAutomask in AFNI to generate automasks if docker is installed.
 
New features of DPARSF_V5.2_210501  (download at http://rfmri.org/dpabi)
1. Users can threshold subjects with bad quality after reorienting.
2. Allow skipping subjects in TRInfo.tsv.
 
New features of DPARSF_V5.1_201001  (download at http://rfmri.org/dpabi)
Fixed a bug in applying slice timing information from DICOM files to DPARSF settings. This bug only affected DPARSF V5.0 while not setting slice timing information (using the default) in slice timing preprocessing. Automatically applying slice timing information from DICOM files missed the unit change for SPM.
 
New features of DPARSF_V5.0_200401  (download at http://rfmri.org/dpabi)
Fixed a bug specific in Windows OS when starting from .nii.gz files: bet fails.
 
New features of DPARSF_V5.0_200301  (download at http://rfmri.org/dpabi)
1. Stability Analysis module was added. You can calculate volume-based and surface-based stability from DPABI->Dynamic & Stability Analyses. You can read our recent work for the details of stability measure: Li, L., Lu, B., Yan, C.G. (2019). Stability of dynamic functional architecture differs between brain networks and states. Neuroimage, 116230, doi:10.1016/j.neuroimage.2019.116230.
2. Field map correction was added, both for DPARSF and DPABISurf. If you want to perform field map Correction, you need to arrange each subject's field map DICOM files in one directory, and then put them in "FieldMap" directory under the working directory. i.e.:';...
    '{Working Directory}\FieldMap\PhaseDiffRaw\Subject001\xxxxx001.dcm';...
    '{Working Directory}\FieldMap\PhaseDiffRaw\Subject001\xxxxx002.dcm';...
    '...';...
    '{Working Directory}\FieldMap\PhaseDiffRaw\Subject002\xxxxx001.dcm';...
    '{Working Directory}\FieldMap\PhaseDiffRaw\Subject002\xxxxx002.dcm';...
    '...';...
    '{Working Directory}\FieldMap\Magnitude1Raw\Subject001\xxxxx001.dcm';...
    '{Working Directory}\FieldMap\Magnitude1Raw\Subject001\xxxxx002.dcm';...
    '...';...
    '{Working Directory}\FieldMap\Magnitude1Raw\Subject002\xxxxx001.dcm';...
    '{Working Directory}\FieldMap\Magnitude1Raw\Subject002\xxxxx002.dcm';...
    '...';...
    '...';...
Then you can click the button of “FieldMap” button to set field map correction parameters. In most cases, you can use the default  “0” value to let the program read the parameters (e.g., echo times) from the DICOM files.
3. Check data organization function added. For the new users of DPARSF and DPABISurf, most of the errors were caused by data organization! Please use DPABI->Utilities->Check Data Organization to check your data organization before running DPARSF or DPABISurf. This program will lead you to organize your data correctly with prompting messages!
4. Slice timing information read from DICOM files. If you are starting with DICOM files, you no longer need to set the slice timing correction parameters. Just leave it as default (slice number: 0), then DPARSF or DPABISurf will read the parameters from DICOM files. This new feature thanks to Dr. Chris Rorden's new dcm2niiX program (version v1.0.20190902).
5. DPARSF V5.0 now is compatible with BIDS format. You can start with BIDS format data by checking checkbox “BIDS to DPARSF” and setting  “Starting Directory Name” to “BIDS”.
 
New features of DPARSF_V4.5_190725  (download at http://rfmri.org/dpabi)
1. For Linux or Mac OS, if FSL is not installed, then DPARSF will call FSL's bet in dpabi docker.
Tips for Linux or Mac O: please start matlab from terminal in order to reach docker in DPABI (e.g., Linux: matlab; Mac: open /Applications/MATLAB_R2018a.app/).
 
New features of DPARSF_V4.4_180801 (download at http://rfmri.org/dpabi):
1. Added a prompt of "Congratulations, the running of DPARSFA is done!!! :)" when DPARSF finishes its processing.
2. Added a new atlas (Schaefer2018_400Parcels_7Networks_order_FSLMNI152_1mm.nii) to the V4 parameters. Please see more details at Schaefer, A., Kong, R., Gordon, E.M., Laumann, T.O., Zuo, X.N., Holmes, A.J., Eickhoff, S.B., Yeo, B.T.T., 2017. Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI. Cereb Cortex, 1-20.
3. The dcm2nii has been updated to the latest version in courtesy of Dr. Chris Rorden. See: Li, X., Morgan, P.S., Ashburner, J., Smith, J., Rorden, C., 2016. The first step for neuroimaging data analysis: DICOM to NIfTI conversion. J Neurosci Methods 264, 47-56.
4. As there were some parallel computing issues in calling outside command, the callings were no longer using parallel computing (i.e., downgrade from parfor to for). These includes the callings of dcm2nii and bet. 
5. Flexibility for concordance was added to the module of Temporal Dynamic Analysis (DPABI_TDA). Users can freely calculate the concordance of any combinations of ALFF, fALFF, ReHo, Degree Centrality, Global Signal Correlation and VMHC.
6. Fixed some compatibility bugs with higher versions of MATLAB. For example, Time Course error in DPABI_VIEW; uimenu parent problem when calling monkey/rat module; errors regard generating pictures for checking normalization in DPARSFA.
7. Tips for calling "bet": You should start matlab from terminal (e.g., Linux: matlab; Mac: open /Applications/MATLAB_R2018a.app/). If you installed FSL5.0, you may also need to run this: source /usr/share/fsl/5.0/etc/fslconf/fsl.sh. In addition, in some Linux versions, you may need to start matlab in this way: LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6" matlab.
 
 
New features of DPARSF_V4.3_170105:
1. DPARSFA V4 Parameters (Default Parameters, also for The R-fMRI Maps Project). For ROI signals extraction, the Power 264 ROIs were added as the 1570~1833 ROIs. (Power_Neuron_264ROIs_Radius5_Mask.nii was added to {DPABI}/Templates/)
2. 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.
3. DPARSF. Add a “Clear All” button in the ROI List GUI for defining ROIs.
 
 
New features DPARSF_V4.2_161201
1. To let the users be more aware what kind of templates they are using, SPM Templates were included under {DPABI}/Templates/ now. If you want to USE YOUR OWN TEMPLATES, please replace the corresponding ones under this directory instead of replacing those under SPM. For example: if you are using normalize by New Segment + DARTEL, please replace {DPABI}/Templates/SPMTemplates/tpm/TPM.nii; If you are using normalize by using EPI template, please replace {DPABI}/Templates/SPMTemplates/toolbox/OldNorm/EPI.nii; If you are using normalize by using T1 image unified segmentation, please replace {DPABI}/Templates/SPMTemplates/toolbox/OldSeg/grey.nii, white.nii, and csf.nii. 
2. DPARSF Windows version. Previously need to run as administrator to get results both with and without global signal regression (GSR). Now such limitation is removed (change mklink to copyfile).
3. DPARSF Advanced Edition Preprocessing for Task fMRI data: For nuisance regression, the option of “Add mean back” is now default. The mean will be added back to the residual after nuisance regression. This is useful for circumstances of ICA or task-based analysis.
4. DPARSFA V4 Parameters (Default Parameters, also for The R-fMRI Maps Project). For ROI signals extraction, the global signal (BrainMask_05_91x109x91.img) was added as the 1569th ROI.
 
 
New features of DPARSF V4.1_160415:
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.
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.
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.
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://rfmri.org/SliceTiming for more details.
 
 
New features of DPARSF_V4.0_151201 (together with DPABI_V2.0_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 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 DPARSF_V3.2_150710:
1. SPM12 Compatible.
2. 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.
3. Fixed a bug in generating Voxel Specific Head Motion: missing gmdmp.
 
New features in DPARSF_V3.1_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.
 
1. 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. New features in 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. New features in 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*".

Licence: GNU General Public Licence (GPL)

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

Gaizhi Li

Wed, 12/02/2015 - 01:59

Permalink

Dr. Yan:
Hi, I used DPARSF, the 1st step epi dicom to nii and remove the first 10 time points, it showed as follows, and in the FunRaw, there are 240 dcm of every sub, in the FunImg, there is only one nii of every subject. I do not know what to do. Thank you so much.
 
??? Undefined function or method 'file2mat' for input arguments of type 'struct'.
 
Error in ==> file_array.subsref>subfun at 80
t = file2mat(sobj,varargin{:});
 
Error in ==> file_array.subsref at 60
    t = subfun(sobj,args{:});
 
Error in ==> nifti.subsref>rec at 219
            t = subsref(t,subs(2:end));
 
Error in ==> nifti.subsref at 45
varargout = rec(opt,subs);
 
Error in ==> DPARSFA_run>(parfor body) at 560
                    y_Write4DNIfTI(Nii.dat(:,:,:,AutoDataProcessParameter.RemoveFirstTimePoints+1:end),Nii,DirImg(1).name);
 
Error in ==> parallel_function at 491
            S = F(base, limit);
 
Error in ==> DPARSFA_run at 528
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in ==> DPARSFA>pushbuttonRun_Callback at 1601
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in ==> gui_mainfcn at 96
        feval(varargin{:});
 
Error in ==> DPARSFA at 33
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callback

Hi,

One .nii is OK, as it contains 240 volumes.

The error you encountered is caused by the conflict between REST and SPM8. REST contains some spm5 files, thus please DO NOT add with subfolders for REST. Or remove REST path to have a try.

Best,

Chao-Gan

Hello,

I am new to DPARSFA and I hope you can help me. I got the following error after specifying my working directory and starting directory (FunImg): "Too many .nii.gz files in each subject's directory, should only keep one 4D .nii.gz file". However, it is only a test run with one subject, so I have one .nii file for this subject in FunImg folder and one .nii.gz file for this subject in the T1Img folder (so one file in each folder in total). What can cause the problem?

 

Thanks a lot!

 

Lisa

Hi, 

Dr Yan,

I have an error in my preprocessing procedure for resting state as below, I use spm8  、  matlab 2007a and DPARSF_V2.3。Is there any problem about this ? Thank you!

 

Running 'New Segment'

Failed  'New Segment'

Error using ==> zeros

Out of memory. Type HELP MEMORY for your options.

In file "F:\MATLAB\R2007a\work\spm8\toolbox\Seg\spm_preproc_write8.m" (v2531), function "rgrid" at line 435.

In file "F:\MATLAB\R2007a\work\spm8\toolbox\Seg\spm_preproc_write8.m" (v2531), function "spm_preproc_write8" at line 241.

In file "F:\MATLAB\R2007a\work\spm8\toolbox\Seg\spm_preproc_run.m" (v2281), function "run_job" at line 112.

In file "F:\MATLAB\R2007a\work\spm8\toolbox\Seg\spm_preproc_run.m" (v2281), function "spm_preproc_run" at line 27.

 

The following modules did not run:

Failed: New Segment

 

??? Error using ==> cfg_util.m>local_runcj at 251

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 ==> DPARSFA>pushbuttonRun_Callback at 1601

    [Error]=DPARSFA_run(handles.Cfg);

 

Error in ==> gui_mainfcn at 95

        feval(varargin{:});

 

Error in ==> DPARSFA at 33

    gui_mainfcn(gui_State, varargin{:});

 

??? Error using ==> DPARSFA('pushbuttonRun_Callback',gcbo,[],guidata(gcbo))

Error using ==> cfg_util.m>local_runcj at 251

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 while evaluating uicontrol Callback

 

>>

Hi,

This is an out of memory error. Please refer to http://rfmri.org/FAQ #2.

Best,

Chao-Gan

 

dongchenjie

Wed, 06/01/2016 - 01:20

Permalink

严老师，您好！

我那个dparsf一运行就报错

并且，MATLAB还会有如下提示

想问下您这是怎么回事？要怎么解决呢？

还有，数据的TR不一样，还能批量处理吗？

谢谢

echoqiu77

Wed, 06/08/2016 - 16:08

Permalink

Hi,

This is the error show in my preprocessing procedure as below, My dpabi version is 4.0,spm is version 8 and the matlab is R2013b, is there any problem about this ?

Error using nifti/subsref>rec (line 104)

BLAS loading error:
dlopen: cannot load any more object with static TLS
 
Error in nifti/subsref (line 45)
varargout = rec(opt,subs);
 
Error in y_Write (line 62)
NIfTIObject.mat=Header.mat;
 
Error in DPARSFA_run>(parfor body) (line 578)
                    y_Write(Nii.dat(:,:,:,AutoDataProcessParameter.RemoveFirstTimePoints+1:end),Nii,DirImg(1).name);
                    
Error in DPARSFA_run (line 546)
        parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in DPARSFA>pushbuttonRun_Callback (line 1761)
    [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:
    Error using  * 
    BLAS loading error:
    dlopen: cannot load any more object with static TLS
 
Error while evaluating uicontrol Callback
 
Error using hgload>localCheckRecursion (line 129)
File
/data/home/qiuh/Downloads/DPABI_V2.0_151201/DPABI_V2.0_151201/DPARSF/DPARSF.fig
recursively loaded itself.
 
Error in hgload (line 42)
 
 
Error in openfig (line 72)
    [fig, savedvisible] = hgload(filename, struct('Visible','off'));
 
Error in gui_mainfcn>local_openfig (line 286)
    gui_hFigure = openfig(name, singleton, visible);
 
Error in gui_mainfcn (line 159)
        gui_hFigure = local_openfig(gui_State.gui_Name, gui_SingletonOpt,
        gui_Visible);
 
Error in DPARSF (line 52)
    gui_mainfcn(gui_State, varargin{:});
 
Error in dpabi>pushbutton_DPARSFB_Callback (line 141)
DPARSF
 
Error in gui_mainfcn (line 96)
        feval(varargin{:});
 
Error in dpabi (line 42)
    gui_mainfcn(gui_State, varargin{:});
 
Error in
@(hObject,eventdata)dpabi('pushbutton_DPARSFB_Callback',hObject,eventdata,guidata(hObject))
 
 
Error using struct2handle
Error while evaluating uicontrol Callback

Thank you!

dongchenjie

Fri, 06/17/2016 - 01:47

Permalink

严老师，您好！

         我想问下，我在workingdirectory里放入了downloadedreorientmats，选了applymats，但为什么reorient那一步还是要手动调整呢？

Hello,

I was using DPARFS to calculate VMHC for resting state fMRI.

I got the results but they look like a mask!

What could i have done wrong? What should i do to fix this?

 

thanks in advance,

 

Walid

 

Hi,

 

Yes, i know it's weird which is why i am asking!

Could you please be more precise? Is there somewhere i should be looking that might have given this output?

I checked my input and i think it is Ok..

Any helpful advice on the matter is highly appreicated!

 

Thank you for your reply. I understand.    

I will share with you the file structure.

dpabi

——————————

Inside dpabi folder

 

 

 

ch2.nii.gz

dirlist.txt

DPARSFA_setting.mat

F.nii

FunRaw

FunRawR

FunRawRC

FunRawRCovs

FunRawRCW

FunRawRCWS

FunRawRCWSF

FunRawRCWSFsym

Masks

PicturesForChkNormalization

RealignParameter

Results

SymmetricGroupT1MeanTemplate

T1Img

T1ImgBet

T1ImgCoreg

T1ImgSegment

T2.nii

 

 

 

————————

Inside the Results folder 

 

 

ALFF_FunRawRCWS

DegreeCentrality_FunRawRCWSF

fALFF_FunRawRCWS

results

VMHC_FunRawRCWSFsym

 

 

 

——————————

 

Inside the results folder

 

DCDegreeCentrality_FunRawRCWSF.nii

VMHCVMHC_FunRawRCWSFsym.nii

zDCDegreeCentrality_FunRawRCWSF.nii

zVMHCVMHC_FunRawRCWSFsym.nii

 

 

 

If you would like to see the setting file, please let me know where to send it because i couldnt attach it here.

 

Thank you again,

 

Walid

 

 

walsin

Thu, 10/06/2016 - 06:30

Permalink

Hello,

 

Inside VMHC_FunRawRCWSFsym  i have files (See below)

dpabi/FunRawRCWSFsym/b105/
dpabi/FunRawRCWSFsym/b106/
.
.
.
.
dpabi/FunRawRCWSFsym/h458/
dpabi/FunRawRCWSFsym/h459/

 

Inside each file i have 

 

FunRawRCWSFsym/b102/sym_Filtered_4DVolume.mat

FunRawRCWSFsym/b102/sym_Filtered_4DVolume.nii
 
 
Is this wrong?
 
 
Shoiuld i copy the sym_Filtered_4DVolume.nii to outside the file e.g. b106 for all file and rename them something like this: VMHCMap_Sub_001.nii?

Hi,

I am using DPARSFA on a Mac with OS Sierra. Unfortunately, I cannot get my segmentation to work (NewSegment+DARTEL)  and I am already getting a warning during coregistration:

Warning: Too many optimisation iterations

> In spm_powell at 46

  In spm_coreg at 149
  In spm_run_coreg at 22
  In matlabbatch/private/cfg_run_cm at 29
  In cfg_util>local_runcj at 1688
  In cfg_util at 959
  In spm_jobman>fill_run_job at 458
  In spm_jobman at 247
  In DPARSFA_run>(parfor body) at 1622
  In parallel_function at 472
  In DPARSFA_run at 1558
  In DPARSFA>pushbuttonRun_Callback at 1779
  In gui_mainfcn at 95
  In DPARSFA at 30 
 
Afterwards, creating the automasks works fine, but then segmantation fails with the following error:
Failed  'Segment'
Error using svd
Input to SVD must not contain NaN or Inf.
In file "/Users/agggold/Desktop/spm12/spm_get_closest_affine.m" (v6137), function "spm_get_closest_affine" at line 68.
In file "/Users/agggold/Desktop/spm12/spm_preproc_write8.m" (v6881), function "spm_preproc_write8" at line 337.
In file "/Users/agggold/Desktop/spm12/spm_preproc_run.m" (v6365), function "run_job" at line 146.
In file "/Users/agggold/Desktop/spm12/spm_preproc_run.m" (v6365), function "spm_preproc_run" at line 41.
In file "/Users/agggold/Desktop/spm12/config/spm_cfg_preproc8.m" (v6798), function "spm_local_preproc_run" at line 418.
 
The following modules did not run:
Failed: Segment
 
Error using MATLABbatch system
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 while evaluating uicontrol Callback
 
I have tried to interactively reorient my FUN and T1 Images, but it doesn't seem to help.
 
Thank you very much for your help!
HG

 

Bliss-shell626

Fri, 12/30/2016 - 02:53

Permalink

严老师：
          您好！我在使用DPARSF做AAL90个脑区的functional connectivity的过程中，Extract ROI finished之后遇到了如下问题：
Load mask "Default".Error using  - 
Matrix dimensions must agree.
 
Error in y_SCA (line 256)
SeedSeries=SeedSeries-repmat(mean(SeedSeries),size(SeedSeries,1),1);
 
Error in DPARSF_run (line 1329)
        y_SCA([AutoDataProcessParameter.DataProcessDir,filesep,FunImgDir,filesep,AutoDataProcessParameter.SubjectID{i}], ...
 
Error in DPARSF>pushbuttonRun_Callback (line 996)
    [Error]=DPARSF_run(handles.Cfg);
 
Error in gui_mainfcn (line 96)
        feval(varargin{:});
 
Error in DPARSF (line 48)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating uicontrol Callback

请问该如何解决呢？之前用SPM预处理数据后得到的图像的dimensions的确是61*73*61。

谢谢

wisepig119

Tue, 02/07/2017 - 03:56

Permalink

Hello, Dr. Yan,

When I used the DPARSF for preprocessing, in the DARTEL, there were many warnings:

Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND =  5.501260e-09.
> In y_regress_ss at 37
  In y_RegressOutImgCovariates at 140
  In DPARSFA_run>(parfor body) at 2640
  In parallel_function>make_general_channel/channel_general at 929
  In remoteParallelFunction at 38 
Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND =  5.501260e-09.
> In y_regress_ss at 37
  In y_RegressOutImgCovariates at 140
  In DPARSFA_run>(parfor body) at 2640
  In parallel_function>make_general_channel/channel_general at 929
  In remoteParallelFunction at 38 
 
What does them mean? Do they affect the results of fMRI data?
Thanks

edit 2017-06-27 T 1457 PDT

It looks like the problem was at some point I unchecked Normalize by mistake, which I realized after loading the autosave*.mat file and seeing that the configuration was slightly different than the screenshot below. Right now I am re-running this, hopefully the problem is fixed.

Thanks,

Felix

 

Hello,

Can someone please help me understand where I can find the wAutoMask files? I ran only preprocessing steps so far (please see screenshot), and wanted to create a group mask before postprocessing. Preprocessing appears to have completed with no problem, resulting in swCovRegressed_4DVolume.nii files within FunImgARCFS\SubjID folders. Do the settings I used result in no wAutoMask files being created, and if so, could you recommend an alternative file type or approach to creating a group mask?

Thanks in advance,

Felix

Hello,

I have used your software to preprocess resting-state data over the years, and your automated preprocessing pipeline DPARSF works very well. I am trying to replicate a finding from my disseration analyses in a new dataset. I have 287 subjects, but did a test on the first three subjects to make sure the automated preprocessing ran smoothly with the latest version of DPARSF (running off DPABI) available on your website. For the test, I selected simple pre-processing: remove first 10 timepoints, slice timing, realignment/motion correction, normalization to EPI template and smoothing at 8 FWHM. DPARSF successfully performed the slice timing and realignment, but then I got this error (see red text below), and it did not complete preprocessing. Do you know what this issue might be? Thanks!

~Stephanie Hare


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Slice Timing'

SPM8: spm_slice_timing (v4310)                     16:08:36 - 11/10/2018
========================================================================
Your TR is 2.0
Done    'Slice Timing'
Done

Slice Timing Setup:S0229 OK


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Slice Timing'

SPM8: spm_slice_timing (v4310)                     16:18:26 - 11/10/2018
========================================================================
Your TR is 2.0
Done    'Slice Timing'
Done

Slice Timing Setup:S0230 OK


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Slice Timing'

SPM8: spm_slice_timing (v4310)                     16:30:13 - 11/10/2018
========================================================================
Your TR is 2.0
Done    'Slice Timing'
Done

Moving Slice Timing Corrected Files:S0230 OKMoving Slice Timing Corrected Files:S0229 OKMoving Slice Timing Corrected Files:S0226 OK
Realign Setup:S0226 OK


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign: Estimate & Reslice'
Done    'Realign: Estimate & Reslice'
Done

Realign Setup:S0229 OK


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign: Estimate & Reslice'
Done    'Realign: Estimate & Reslice'
Done

Realign Setup:S0230 OK


------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign: Estimate & Reslice'
Done    'Realign: Estimate & Reslice'
Done

Moving Head Motion Corrected Files:S0230 OKMoving Head Motion Corrected Files:S0229 OKMoving Head Motion Corrected Files:S0226 OK
Reorienting Functional Images Interactively for S0226:
Reference to non-existent field 'ReorientMat'.

Error in DPARSFA_run (line 1196)
        mat=y_spm_image_Parameters.ReorientMat;

Error in DPARSF_run (line 113)
[Error] = DPARSFA_run(Cfg);

Error in DPARSF>pushbuttonRun_Callback (line 1154)
    [Error]=DPARSF_run(handles.Cfg);

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

Error in DPARSF (line 52)
    gui_mainfcn(gui_State, varargin{:});
 
Error using drawnow
Error while evaluating uicontrol Callback

严老师，

        您好！我想做的是基于DPARSF软件，将预处理后的脑功能网络图像进行基于体素的相关分析，对于每一被试，计算全脑任意一对体素时间序列间的Pearson相关系数，生成一个高维（如70831*70831）的相关矩阵。目前，我可以提取到如AAL的90*90的相关矩阵，Power_Neuron_264ROIs的264*264的相关矩阵，但提取不到高维的关于体素级的相关矩阵。这个高维的体素级脑网络相关矩阵该如何提取到？

mrym_masoudi

Tue, 12/18/2018 - 14:31

Permalink

Hi

I faced an error processing my data. while it was converting t1 dicom to nifti, I got this error 

I am using MATLAB R2018b and SPM12 . my data is from ADNI database.

would you please help me?

reading preferences file DCM2NII.INI 
Validating 6720 potential DICOM images. 
Found 6720 DICOM images. 
Converting 6720/6720  volumes: 140 
ADNI_002_S_1268_MR_Resting_State_fMRI_br_raw_20110413181332693_1_S104191_I227595.dcm->20110413_141227RestingStatefMRI002S1268s501a1005.nii 
 brightest voxel was 3672: data will be saved as 16-bit signed integer. 
Saving C:\USERS\MM\DOCUMENTS\MATLAB\TOOLS\PRACTICE2\FUNIMG\S104191\20110413_141227RestingStatefMRI002S1268s501a1005.nii 
Time elapsed 3515ms 
Converting Functional Images:S104191 OKChris Rorden's dcm2nii :: 2MAY2016 64bit BSD License  :: (upgrade to dcm2niix suggested) 
reading preferences file DCM2NII.INI 
Validating 6720 potential DICOM images. 
Found 6720 DICOM images. 
Converting 6720/6720  volumes: 140 
ADNI_136_S_0107_MR_Resting_State_fMRI_br_raw_20120910171226224_1_S166728_I332647.dcm->20120906_092942RestingStatefMRI136S0107s501a1005.nii 
 brightest voxel was 3302: data will be saved as 16-bit signed integer. 
Saving C:\USERS\MM\DOCUMENTS\MATLAB\TOOLS\PRACTICE2\FUNIMG\S166728\20120906_092942RestingStatefMRI136S0107s501a1005.nii 
Time elapsed 3875ms 
Converting Functional Images:S166728 OK
Index exceeds array bounds.
 
Error in DPARSFA_run (line 275)
        InputFilename=[AutoDataProcessParameter.DataProcessDir,filesep,'T1Raw',filesep,AutoDataProcessParameter.SubjectID{i},filesep,DirDCM(StartIndex).name];
 
Error in DPARSFA>pushbuttonRun_Callback (line 1795)
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating UIControl Callback.

puyunfashi

Wed, 12/19/2018 - 01:25

Permalink

Please check very carefully your FunImg directory about 1) whether there is empty folder 2) whether there are  folders that contain different number of dicom files

Dear Professor Yan
 
Thank you for your useful toolbox.
 
I have a problem when I generate the auto mask . and even I check off it I still have this probllem and can not conduct other following processing. Could you kindly find the reason. Thank you 
 
Your sincerely Wang
 
Here is the error message. I use the latest version.
 
Reading images from "D:\ANA\FunImgAR\004\ra20140529_135907ep2dboldPA40sl25Ascend40529201s003a001.nii" etc.
 
Reading images from "D:\ANA\FunImgAR\005\ra20140529_155642ep2dboldPA40sl25Ascend40529202s003a001.nii" etc.
Error using w_ClipLevel (line 37)
Index in position 2 is invalid. Array indices must be positive integers or logical values.
 
Error in w_Automask (line 33)
    clip_fixed=w_ClipLevel(0.5, MeanAbsVolume);
 
Error in DPARSFA_run (line 1821)
    parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in DPARSFA>pushbuttonRun_Callback (line 1795)
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating UIControl Callback.
 

shuxia_yao

Wed, 07/24/2019 - 09:36

Permalink

Hi Dr. Yan,

I am running the "Normalize to Symmetric Template" before the VMHC analysis and meet an error as followed for some of my subjects :

------------------------------------------------------
Failed  'Normalise: Estimate & Write'
Error using spm_affreg>error_message (line 474)
insufficient image overlap
In file "C:\Program Files\MATLAB\matlab tools\fMRI_toolbox\Matlab tools\spm8\spm_affreg.m" (v4152), function "error_message" at line 474.
In file "C:\Program Files\MATLAB\matlab tools\fMRI_toolbox\Matlab tools\spm8\spm_affreg.m" (v4152), function "spm_affreg" at line 177.
In file "C:\Program Files\MATLAB\matlab tools\fMRI_toolbox\Matlab tools\spm8\spm_normalise.m" (v4185), function "spm_normalise" at line 176.
In file "C:\Program Files\MATLAB\matlab tools\fMRI_toolbox\Matlab tools\spm8\config\spm_run_normalise_estwrite.m" (v4152), function "spm_run_normalise_estwrite" at line 22.
 
The following modules did not run:
Failed: Normalise: Estimate & Write
 
Running 'Normalise: Estimate & Write'
Smoothing by 0 & 8mm..
Coarse Affine Registration..
Running 'Normalise: Estimate & Write'
Smoothing by 0 & 8mm..
Coarse Affine Registration..
Error using cfg_util (line 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 (line 217)
 
Error in DPARSFA_run (line 4201)
    parfor i=1:AutoDataProcessParameter.SubjectNum
 
Error in DPARSFA>pushbuttonRun_Callback (line 1786)
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating UIControl Callback
---------------------------------------------------------------------
the preprocessing of these subjects looks good including normalization. I also tried some other dparsf version and met simillar error. 
Could you give me some help 0n this error?
Thanks in advance!
Shuxia
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