DPABI/DPABISurf/DPARSF

Problem with normalization

Submitted by Stephanie on
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DPABI/DPABISurf/DPARSF

Hi,

I am using the DPARSF 2.2 version using DARTEL for normalization. Unfortunatly after normalization my functional images (for almost all subjects) show random spots (a couple of voxels) with extremly reduced intensity values. This can be seen as black spots when checking "PicturesForChkNormalization". Prior to normalization, these spots are not visible.

I attached a pdf file showing my DPARSF setting and a couple of images from different subjects. 

Thanks in advance for your help.

Regards,

Stephanie

Reorienting matrices for online data

Submitted by YAN Chao-Gan on
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DPABI/DPABISurf/DPARSF

Given the amount of time and effort for interactive reorienting, here we released the reorient matrices for some of the publicly released data. Please download and unzip the related file, and then put the folder of “DownloadedReorientMats” under your working directory.

1. Autism Brain Imaging Data Exchange (ABIDE) (Di Martino et al., in press) (http://fcon_1000.projects.nitrc.org/indi/abide/). Please download: DownloadedReorientMats_ABIDE.zip.

Data Processing Assistant for Resting-State fMRI (DPARSF) V2.3

Submitted by YAN Chao-Gan on
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DPABI/DPABISurf/DPARSF

 

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, 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 COURSEto know more about how to use this software. Add DPARSF's directory to MATLAB's path and enter "DPARSF" or "DPARSFA" in the command window to enjoy DPARSF basic edition or advanced edition.

The latest release is DPARSF_V2.3_130615.  

DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

 

 

New features of DPARSF_V2.3_130615:
1. Apply downloaded reorient matrices. Given the amount of time and effort for interactive reorienting, the reorient matrices for online data such as 1000 Functional Connectomes Project (FCP) (Biswal et al., 2010) and Autism Brain Imaging Data Exchange (ABIDE) (Di Martino et al., 2013) could be downloaded and applied automatically. Please find here for “DownloadedReorientMats”, and then tick the checkbox "Apply Mats".
2. Save information of TR, Slice Number, Time Points and Voxel Size into TRInfo.tsv (under working directory) file for checking data correctness.
3. The slice order type could be specified for each participant into SliceOrderInfo.tsv (under working directory) file, thus allow different slice timing correction for different participants in a batch mode. Please find instructions for setting SliceOrderInfo.tsv from {DPARSF}/Docs/SliceOrderInfo.tsv_Instruction.txt.
4. The output format of DICOM to NIfTI were changed to 4D .nii images.
5. The midline of VMHC results were set to zero.
 

How to convert from voxel index to MNI coordinates and vice versa.

Submitted by YAN Chao-Gan on
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DPABI/DPABISurf/DPARSF

Please see the figure below (aal.nii opened by MRIcroN).
The MNI coordinates of the current position is -66 -92 -40, and its value is 0. (-66x-92x-40= 0 on the titile).
The voxel index is 25 34 32. (X 25 Y 34 Z 32).

1. Read the file header:

[Data Header]=y_Read('aal.nii');

2. Convert from voxel index to MNI coordinates:
MNI_Coordinates = Header.mat*[25;34;32;1]
MNI_Coordinates =
-66
-92
-40
1

Names of ROIs

Submitted by Timhahn on
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DPABI/DPABISurf/DPARSF
 Dear all -
I extracted the connectivity matrix between all ROIs from the atlases provided with DPARSFA (AAL, Craddock, Dosenbach, ...). How do I find out the name of each ROI for each atlas? For the Harvard Oxford Atlas a file with anatomical labels is provided, but I'm not sure on how to use that.
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