Use scripts to generate montage images in DPABI_VIEW

1. Open DPABI_VIEW, and load your images and setup.

Or you can use w_Call_DPABI_VIEW.m to setup automatically.

%H = w_Call_DPABI_VIEW(BrainVolume,NMin,PMin,ClusterSize,ConnectivityCriterion,UnderlayFileName,ColorMap,NMax,PMax,H,Transparency,Position,BrainHeader)

DPARSFA Output File Summary

As many users of DPARSFA were confused about the meaning of DPARSFA Output file, this summary was compiled according to the video on

DPARSFA_Autosaved_xxx -- DPARSFA setting log file.

FunRaw -- Raw functional images. 

FunImg -- Functional images in NIFTI format.

FunImgA -- This file contains the functional images after slice timing.

Permutation Test in DPABI

DPABI has implemented a convenient way to perform permutation test in Statistical Analysis, which is based on the PALM package (Winkler et al., 2016).

Configurations for DPARSFA_run

You can run DPARSFA_run independently from the GUI to process your data. You can use the GUI to define the configuration parameters (Cfg/AutoDataProcessParameter). Or you can learn the structure as follows. 

Repetition Time (TR)

Repetition Time (TR) is the amount of time that passes between consecutive acquired brain volumes. The value (in seconds) is used for slice timing correction and filtering.  A specific TR value should be set in the text box.

Alternatively, if the TR value were set to 0 in the text box, the TR information would be read automatically from the NIfTI headers (please make sure the TR information in NIfTI files is correct). The retrieved TR information would be saved in TRInfo.tsv for future usage.

Extract ROI Time Courses (ROI-wise functional connectivity)

In DPARSF, users could extract ROI time courses (simultaneously have the ROI-wise functional connectivity) by check "Extract ROI time courses" checkbox and "Define ROI".

DPARSF extracts the ROI time courses based on the data defined by the "Starting Directory Name". The results are output at "Results/ROISignals_FunImgXXX":

ROI_OrderKey_SubXXX.tsv: The ROI definition for a given subject SubXXX.

Slice Timing

Most fMRI data are acquired using two-dimensional pulse sequences that acquire images one slice at a time, thus all slices are acquired at different time within a repeat time (TR). Timing differences are especially problematic for longer TR. Hence the differences in image acquisition time between slices need to be corrected. The number of slices, slice order and reference slice need to be specified, then DPARSF will do slice timing by calling functions in SPM.

Time Points

Time Points is the number of time points (volumes) of the functional data. 

Subject List

Subject List is the list of subjects whose data needs to be processed.

After setting the Starting Directory Name at the bottom right of DPARSF, the program will read the directories under the Starting Directory (E.g., FunRaw or FunImg), and put them in to the Participants List field.

Working Directory

Working Directory is a common concept within DPARSF.

In DPARSF, Working Directory means the upper directory of FunRaw/T1Raw/FunImg/T1Img etc. All the results will be generated under the Working Directory.

The data organization under the working directory should be:


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