Data Processing Assistant for Resting-State fMRI (DPARSF) V1.0

Data Processing Assistant for Resting-State fMRI (DPARSF) is a convenient plug-in software based on SPM and REST. 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, nomalize, smooth) data, FC, ReHo, ALFF and fALFF 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 AAL or ROI time courses (or extract Gray Matter Volume of AAL regions, command line only) efficiently if you want to perform small-world analysis. This software is very easy to use, just click on buttons if you are not sure what it means, popup tips would tell you what you need to do. You also can download a MULTIMEDIA COURSE to know more about how to use this software. Add DPARSF's directory to MATLAB's path and enter "DPARSF" in the command window of MATLAB to enjoy it.

The latest release is DPARSF_V1.0_100510




DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

New features of DPARSF_V1.0_100510:
1. Added a right-click menu to delete all the participants' ID.
2. Fixed a bug in converting DICOM files to NIfTI in Windows 7, thanks to Prof. Chris Rorden's new dcm2nii.
3. Now will detect if co* T1 image (T1 image which is reoriented to the nearest orthogonal direction to 'canonical space' and removed excess air surrounding the individual as well as parts of the neck below the cerebellum) exists before normalization by using T1 image unified segmentation. T1 image without 'co' is also allowed in the analysis now.

New features of DPARSF_V1.0_100420:
1. After extracting ROI time courses, not just functional connectivity will be calculated, but also transform the r values to z values by Fisher's z transformation.
2. Fixed a bug in generating pictures for checking normalization when the bounding box is not [-90 -126 -72;90 90 108].

New features of DPARSF_V1.0_100201:
1. Save the configuration parameters automatically.
2. Fixed the bug in converting DICOM files to NIfTI files when DPARSF stored under C:\Program Files\Matlab\Toolbox.
3. Fixed the bug in converting DICOM files to NIfTI files when the filename without extension.

New features of DPARSF_V1.0_091215:
1. Also can regress out other kind of covariates other than head motion parameters, Global mean signal, White matter signal and Cerebrospinal fluid signal.

New features of DPARSF_V1.0_091201:
1. Added an option to choose different Affine Regularisation in Segmentation: East Asian brains (eastern) or European brains (mni). The interpretation of this option from SPM is: “If you can approximately align your images prior to running Segment, then this will increase the robustness of segmentation. Another thing that may help would be to change the regularisation of the initial affine registration, via Segment->Custom->Affine Regularisation. If you set this to "ICBM space template - East Asian brains (or European brains)", then the algorithm will make use of knowledge about the approximate variability to expect among the width/length etc of the brains of the population.” “The prior probability distribution for affine registration of East-Asian brains to MNI space was derived from 65 seg_inv_sn.mat files from Singapore. The distribution of affine transforms of European brains was estimated from: Incorporating Prior Knowledge into Image Registration NeuroImage, Volume 6, Issue 4, November 1997, Pages 344-352 J. Ashburner, P. Neelin, D. L. Collins, A. Evans, K. Friston.”
2. Added a Utility: change the Prefix of Images since DPARSF need some special prefixes in some cases. For example, if you do not have T1 DICOM files and your T1 NIFTI files are not initiated with “co”, then you can use this utility to add the “co” prefix to let DPARSF perform normalization based on segmentation of T1 images.
3. Added a popup menu to delete selected subject by right click.
4. Added a checkbox for removing first time points.
5. Added a function to close wait bar when program finished.
 
New features of DPARSF_V1.0Beta_091001:

1. SPM8 compatible.
2. Generate the pictures (output in {Working Directory}\PicturesForChkNormalization\) for checking normalization.

New features of DPARSF_V1.0Beta_090911:
1. Fixed the bug of setting user's defined mask.

New features of DPARSF_V1.0Beta_090901:
1. Fixed the bug of setting FWHM kernel of smooth.
2. Smooth the mReHo results.
3. Remove any number of the first time points.

New features of DPARSF_V1.0Beta_090713:
1. mReHo - 1, mALFF - 1, mfALFF - 1 function.
2. Creating report for excessive head motion subjects excluding.

New features of DPARSF_V1.0Beta_090701:
1. Linux compatible.
 

DPARSF's standard processing steps:
1. Convert DICOM files to NIFTI images.
2. Remove First 10 (more or less) Time Points.
3. Slice Timing.
4. Realign.
5. Normalize.
6. Smooth (optional).
7. Detrend.
8. Filter.
9. Calculate ReHo, ALFF, fALFF (optional).
10. Regress out the Covariables (optional).
11. Calculate Functional Connectivity (optional).
12. Extract AAL or ROI time courses for further analysis (optional).
13. Extract Gray Matter Volume of AAL regions for further analysis (optional, command line only).

If you think DPARSF is useful for your work, citing it in your paper would be greatly appreciated.
Something like "... preprocessing were carried out using Statistical Parametric Mapping (SPM5, http://www.fil.ion.ucl.ac.uk/spm) and Data Processing Assistant for Resting-State fMRI (DPARSF) (Yan and Zang, 2010) ..." in your method session would be fine. If FC, ReHo, ALFF or fALFF is computed, please also cite Resting-State fMRI Data Analysis Toolkit (REST, by Song et al., http://www.restfmri.net).
Reference: Yan C and Zang Y (2010) DPARSF: a MATLAB toolbox for "pipeline" data analysis of resting-state fMRI. Front. Syst. Neurosci. 4:13. doi:10.3389/fnsys.2010.00013

DPARSF i

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在用dparsf时发现了两个小问题,请尽快解决!
1 在更改FWHM时(如将4 4 4改为8 8 8)会出现错误提示,具体见下:
Undefined function or variable 'VoxSize'.

Error in ==> DPARSF>editFWHM_Callback at 425
    handles.Cfg.Smooth.FWHM =eval(['[',VoxSize,']']);

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

Error in ==> DPARSF at 31
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uicontrol Callba           不过这个问题已经由朱老师组的孟同学解决掉了。
2 不能自动删除前十个时间点的数据,而且和右侧输入的时间点数不能匹配。比如如果你有200个时间点,如果你选择了去除前十个时间点这一项,你必须在time points处填210,不然就运行不下去。而且在删除前10个时间点时软件会误将前20个时间点的img文件删掉,而保留hdr文件,导致软件也不能正常运行下去,只能手动一个一个删除前十个时间点比较麻烦!
希望能尽快解决!谢谢。
 

Thanks for your report!
Please download the latest release.
Best wishes!

Information of 90 AAL Regions used in DPARSF:






volume-based ROI

volume-based ROI
Labels Regions Regions abbr. x(voxel) y(voxel) z(voxel) x(mm) y(mm) z(mm)
1 Precentral_L Precental gyrus PreCG.L 51 120 123 -38.65 -5.68 50.94
2 Precentral_R Precental gyrus PreCG.R 131 118 124 41.37 -8.21 52.09
3 Frontal_Sup_L Superior frontal gyrus, dorsolateral SFGdor.L 72 161 114 -18.45 34.81 42.20
4 Frontal_Sup_R Superior frontal gyrus, dorsolateral SFGdor.R 112 157 116 21.90 31.12 43.82
5 Frontal_Sup_Orb_L Superior frontal gyrus, orbital part ORBsup.L 73 173 59 -16.56 47.32 -13.31
6 Frontal_Sup_Orb_R Superior frontal gyrus, orbital part ORBsup.R 108 174 58 18.49 48.10 -14.02
7 Frontal_Mid_L Middle frontal gyrus MFG.L 57 159 107 -33.43 32.73 35.46
8 Frontal_Mid_R Middle frontal gyrus MFG.R 128 159 106 37.59 33.06 34.04
9 Frontal_Mid_Orb_L Middle frontal gyrus, orbital part ORBmid.L 59 176 62 -30.65 50.43 -9.62
10 Frontal_Mid_Orb_R Middle frontal gyrus, orbital part ORBmid.R 123 179 61 33.18 52.59 -10.73
11 Frontal_Inf_Oper_L Inferior frontal gyrus, opercular part IFGoperc.L 42 139 91 -48.43 12.73 19.02
12 Frontal_Inf_Oper_R Inferior frontal gyrus, opercular part IFGoperc.R 140 141 93 50.20 14.98 21.41
13 Frontal_Inf_Tri_L Inferior frontal gyrus, triangular part IFGtriang.L 44 156 86 -45.58 29.91 13.99
14 Frontal_Inf_Tri_R Inferior frontal gyrus, triangular part IFGtriang.R 140 156 86 50.33 30.16 14.17
15 Frontal_Inf_Orb_L Inferior frontal gyrus, orbital part ORBinf.L 54 157 60 -35.98 30.71 -12.11
16 Frontal_Inf_Orb_R Inferior frontal gyrus, orbital part ORBinf.R 131 158 60 41.22 32.23 -11.91
17 Rolandic_Oper_L Rolandic operculum ROL.L 43 118 86 -47.16 -8.48 13.95
18 Rolandic_Oper_R Rolandic operculum ROL.R 143 120 87 52.65 -6.25 14.63
19 Supp_Motor_Area_L Supplementary motor area SMA.L 85 131 133 -5.32 4.85 61.38
20 Supp_Motor_Area_R Supplementary motor area SMA.R 99 126 134 8.62 0.17 61.85
21 Olfactory_L Olfactory cortex OLF.L 82 141 61 -8.06 15.05 -11.46
22 Olfactory_R Olfactory cortex OLF.R 100 142 61 10.43 15.91 -11.26
23 Frontal_Sup_Medial_L Superior frontal gyrus, medial SFGmed.L 85 175 103 -4.80 49.17 30.89
24 Frontal_Sup_Medial_R Superior frontal gyrus, medial SFGmed.R 99 177 102 9.10 50.84 30.22
25 Frontal_Mid_Orb_L Superior frontal gyrus, medial orbital ORBsupmed.L 85 180 65 -5.17 54.06 -7.40
26 Frontal_Mid_Orb_R Superior frontal gyrus, medial orbital ORBsupmed.R 98 178 65 8.16 51.67 -7.13
27 Rectus_L Gyrus rectus REC.L 85 163 54 -5.08 37.07 -18.14
28 Rectus_R Gyrus rectus REC.R 98 162 54 8.35 35.64 -18.04
29 Insula_L Insula INS.L 55 133 75 -35.13 6.65 3.44
30 Insula_R Insula INS.R 129 132 74 39.02 6.25 2.08
31 Cingulum_Ant_L Anterior cingulate and paracingulate gyri ACG.L 86 161 86 -4.04 35.40 13.95
32 Cingulum_Ant_R Anterior cingulate and paracingulate gyri ACG.R 98 163 88 8.46 37.01 15.84
33 Cingulum_Mid_L Median cingulate and paracingulate gyri DCG.L 85 111 114 -5.48 -14.92 41.57
34 Cingulum_Mid_R Median cingulate and paracingulate gyri DCG.R 98 117 112 8.02 -8.83 39.79
35 Cingulum_Post_L Posterior cingulate gyrus PCG.L 85 83 97 -4.85 -42.92 24.67
36 Cingulum_Post_R Posterior cingulate gyrus PCG.R 97 84 94 7.44 -41.81 21.87
37 Hippocampus_L Hippocampus HIP.L 65 105 62 -25.03 -20.74 -10.13
38 Hippocampus_R Hippocampus HIP.R 119 106 62 29.23 -19.78 -10.33
39 ParaHippocampal_L Parahippocampal gyrus PHG.L 69 110 51 -21.17 -15.95 -20.70
40 ParaHippocampal_R Parahippocampal gyrus PHG.R 115 111 52 25.38 -15.15 -20.47
41 Amygdala_L Amygdala AMYG.L 67 125 55 -23.27 -0.67 -17.14
42 Amygdala_R Amygdala AMYG.R 117 127 54 27.32 0.64 -17.50
43 Calcarine_L Calcarine fissure and surrounding cortex CAL.L 83 47 78 -7.14 -78.67 6.44
44 Calcarine_R Calcarine fissure and surrounding cortex CAL.R 106 53 81 15.99 -73.15 9.40
45 Cuneus_L Cuneus CUN.L 84 46 99 -5.93 -80.13 27.22
46 Cuneus_R Cuneus CUN.R 104 47 100 13.51 -79.36 28.23
47 Lingual_L Lingual gyrus LING.L 75 58 67 -14.62 -67.56 -4.63
48 Lingual_R Lingual gyrus LING.R 106 59 68 16.29 -66.93 -3.87
49 Occipital_Sup_L Superior occipital gyrus SOG.L 73 42 100 -16.54 -84.26 28.17
50 Occipital_Sup_R Superior occipital gyrus SOG.R 114 45 103 24.29 -80.85 30.59
51 Occipital_Mid_L Middle occipital gyrus MOG.L 58 45 88 -32.39 -80.73 16.11
52 Occipital_Mid_R Middle occipital gyrus MOG.R 127 46 91 37.39 -79.70 19.42
53 Occipital_Inf_L Inferior occipital gyrus IOG.L 54 48 64 -36.36 -78.29 -7.84
54 Occipital_Inf_R Inferior occipital gyrus IOG.R 128 44 64 38.16 -81.99 -7.61
55 Fusiform_L Fusiform gyrus FFG.L 59 86 52 -31.16 -40.30 -20.23
56 Fusiform_R Fusiform gyrus FFG.R 124 87 52 33.97 -39.10 -20.18
57 Postcentral_L Postcentral gyrus PoCG.L 48 103 121 -42.46 -22.63 48.92
58 Postcentral_R Postcentral gyrus PoCG.R 131 101 125 41.43 -25.49 52.55
59 Parietal_Sup_L Superior parietal gyrus SPG.L 67 66 131 -23.45 -59.56 58.96
60 Parietal_Sup_R Superior parietal gyrus SPG.R 116 67 134 26.11 -59.18 62.06
61 Parietal_Inf_L Inferior parietal, but supramarginal and angular gyri IPL.L 47 80 119 -42.80 -45.82 46.74
62 Parietal_Inf_R Inferior parietal, but supramarginal and angular gyri IPL.R 136 80 122 46.46 -46.29 49.54
63 SupraMarginal_L Supramarginal gyrus SMG.L 34 92 102 -55.79 -33.64 30.45
64 SupraMarginal_R Supramarginal gyrus SMG.R 148 94 106 57.61 -31.50 34.48
65 Angular_L Angular gyrus ANG.L 46 65 108 -44.14 -60.82 35.59
66 Angular_R Angular gyrus ANG.R 136 66 111 45.51 -59.98 38.63
67 Precuneus_L Precuneus PCUN.L 83 70 120 -7.24 -56.07 48.01
68 Precuneus_R Precuneus PCUN.R 100 70 116 9.98 -56.05 43.77
69 Paracentral_Lobule_L Paracentral lobule PCL.L 82 101 142 -7.63 -25.36 70.07
70 Paracentral_Lobule_R Paracentral lobule PCL.R 97 94 140 7.48 -31.59 68.09
71 Caudate_L Caudate nucleus CAU.L 79 137 81 -11.46 11.00 9.24
72 Caudate_R Caudate nucleus CAU.R 105 138 81 14.84 12.07 9.42
73 Putamen_L Lenticular nucleus, putamen PUT.L 66 130 74 -23.91 3.86 2.40
74 Putamen_R Lenticular nucleus, putamen PUT.R 118 131 74 27.78 4.91 2.46
75 Pallidum_L Lenticular nucleus, pallidum PAL.L 72 126 72 -17.75 -0.03 0.21
76 Pallidum_R Lenticular nucleus, pallidum PAL.R 111 126 72 21.20 0.18 0.23
77 Thalamus_L Thalamus THA.L 79 108 80 -10.85 -17.56 7.98
78 Thalamus_R Thalamus THA.R 103 108 80 13.00 -17.55 8.09
79 Heschl_L Heschl gyrus HES.L 48 107 82 -41.99 -18.88 9.98
80 Heschl_R Heschl gyrus HES.R 136 109 82 45.86 -17.15 10.41
81 Temporal_Sup_L Superior temporal gyrus STG.L 37 105 79 -53.16 -20.68 7.13
82 Temporal_Sup_R Superior temporal gyrus STG.R 148 104 79 58.15 -21.78 6.80
83 Temporal_Pole_Sup_L Temporal pole: superior temporal gyrus TPOsup.L 50 141 52 -39.88 15.14 -20.18
84 Temporal_Pole_Sup_R Temporal pole: superior temporal gyrus TPOsup.R 138 141 55 48.25 14.75 -16.86
85 Temporal_Mid_L Middle temporal gyrus MTG.L 34 92 70 -55.52 -33.80 -2.20
86 Temporal_Mid_R Middle temporal gyrus MTG.R 147 89 71 57.47 -37.23 -1.47
87 Temporal_Pole_Mid_L Temporal pole: middle temporal gyrus TPOmid.L 54 141 38 -36.32 14.59 -34.08
88 Temporal_Pole_Mid_R Temporal pole: middle temporal gyrus TPOmid.R 134 141 40 44.22 14.55 -32.23
89 Temporal_Inf_L Inferior temporal gyrus ITG.L 40 98 49 -49.77 -28.05 -23.17
90 Temporal_Inf_R Inferior temporal gyrus ITG.R 144 95 50 53.69 -31.07 -22.32

Also, the information of the 116 AAL regions from MRIcroN:

1 Precentral_L 2001
2 Precentral_R 2002
3 Frontal_Sup_L 2101
4 Frontal_Sup_R 2102
5 Frontal_Sup_Orb_L 2111
6 Frontal_Sup_Orb_R 2112
7 Frontal_Mid_L 2201
8 Frontal_Mid_R 2202
9 Frontal_Mid_Orb_L 2211
10 Frontal_Mid_Orb_R 2212
11 Frontal_Inf_Oper_L 2301
12 Frontal_Inf_Oper_R 2302
13 Frontal_Inf_Tri_L 2311
14 Frontal_Inf_Tri_R 2312
15 Frontal_Inf_Orb_L 2321
16 Frontal_Inf_Orb_R 2322
17 Rolandic_Oper_L 2331
18 Rolandic_Oper_R 2332
19 Supp_Motor_Area_L 2401
20 Supp_Motor_Area_R 2402
21 Olfactory_L 2501
22 Olfactory_R 2502
23 Frontal_Sup_Medial_L 2601
24 Frontal_Sup_Medial_R 2602
25 Frontal_Med_Orb_L 2611
26 Frontal_Med_Orb_R 2612
27 Rectus_L 2701
28 Rectus_R 2702
29 Insula_L 3001
30 Insula_R 3002
31 Cingulum_Ant_L 4001
32 Cingulum_Ant_R 4002
33 Cingulum_Mid_L 4011
34 Cingulum_Mid_R 4012
35 Cingulum_Post_L 4021
36 Cingulum_Post_R 4022
37 Hippocampus_L 4101
38 Hippocampus_R 4102
39 ParaHippocampal_L 4111
40 ParaHippocampal_R 4112
41 Amygdala_L 4201
42 Amygdala_R 4202
43 Calcarine_L 5001
44 Calcarine_R 5002
45 Cuneus_L 5011
46 Cuneus_R 5012
47 Lingual_L 5021
48 Lingual_R 5022
49 Occipital_Sup_L 5101
50 Occipital_Sup_R 5102
51 Occipital_Mid_L 5201
52 Occipital_Mid_R 5202
53 Occipital_Inf_L 5301
54 Occipital_Inf_R 5302
55 Fusiform_L 5401
56 Fusiform_R 5402
57 Postcentral_L 6001
58 Postcentral_R 6002
59 Parietal_Sup_L 6101
60 Parietal_Sup_R 6102
61 Parietal_Inf_L 6201
62 Parietal_Inf_R 6202
63 SupraMarginal_L 6211
64 SupraMarginal_R 6212
65 Angular_L 6221
66 Angular_R 6222
67 Precuneus_L 6301
68 Precuneus_R 6302
69 Paracentral_Lobule_L 6401
70 Paracentral_Lobule_R 6402
71 Caudate_L 7001
72 Caudate_R 7002
73 Putamen_L 7011
74 Putamen_R 7012
75 Pallidum_L 7021
76 Pallidum_R 7022
77 Thalamus_L 7101
78 Thalamus_R 7102
79 Heschl_L 8101
80 Heschl_R 8102
81 Temporal_Sup_L 8111
82 Temporal_Sup_R 8112
83 Temporal_Pole_Sup_L 8121
84 Temporal_Pole_Sup_R 8122
85 Temporal_Mid_L 8201
86 Temporal_Mid_R 8202
87 Temporal_Pole_Mid_L 8211
88 Temporal_Pole_Mid_R 8212
89 Temporal_Inf_L 8301
90 Temporal_Inf_R 8302
91 Cerebelum_Crus1_L 9001
92 Cerebelum_Crus1_R 9002
93 Cerebelum_Crus2_L 9011
94 Cerebelum_Crus2_R 9012
95 Cerebelum_3_L 9021
96 Cerebelum_3_R 9022
97 Cerebelum_4_5_L 9031
98 Cerebelum_4_5_R 9032
99 Cerebelum_6_L 9041
100 Cerebelum_6_R 9042
101 Cerebelum_7b_L 9051
102 Cerebelum_7b_R 9052
103 Cerebelum_8_L 9061
104 Cerebelum_8_R 9062
105 Cerebelum_9_L 9071
106 Cerebelum_9_R 9072
107 Cerebelum_10_L 9081
108 Cerebelum_10_R 9082
109 Vermis_1_2 9100
110 Vermis_3 9110
111 Vermis_4_5 9120
112 Vermis_6 9130
113 Vermis_7 9140
114 Vermis_8 9150
115 Vermis_9 9160
116 Vermis_10 9170