REST (or DPARSF) toolbox: Getting Started

This pages describes how to manually get started with the REST toolbox, used for analyzing resting state fMRI (rsfMRI).

mricron is a free tool for viewing nifti files. It will download (in a zipped format) and "mricron" folder with the program files. I like to copy this into C:\Program FIles\, and make a shortcut/taskbar link to the mricron.exe file.
IrfanView is a free bitmap editor - like Paint but way better. Download & install (may as well select 64-bit version), then download & install Plugs-Ins (also 64-bit). This will not recognise files with a .dcm extension as DICOM files, and open them.
SPM (MATLAB program) - download SPM with Paul's custom "CSPM" toolbox
- Download from https://drive.google.com/open?id=0BzUB3_5SN2mlVWtjZ0hCZi1pdjg
- Change file permissions to read/write (remove read-only flag - right-click over spm12 folder, Properties, unselect Read-Only, click OK - see snapshot top-right of this page.
- Example path: C:\matlab\spm12
REST toolbox - download latest and store separately for now. (Later on, this will be inside SPM, but for this stage keep it separate.)
- It's possible this needs to run with SPM - talk with Paul if so.

Start with raw data; save in one location. This will include subject folders, 7000's for controls, and 9000's for HIV.

Copy to "Working" folder; this will be used for converting from DICOM to nifti formats.

Open SPM: open MATLAB, go to spm12 folder, add to path:

>> cd c:\matlab\spm12
>> addpath(pwd)
>> spm fmri

Next three steps, see snapshots on right
Start CSPM (under Toolbox drop-down); this will open a GUI after a few seconds

Click "DICOM rename/convert" - top left button of CSPM GUI

Put in the path of the raw DICOM fiels (e.g., D:\Working\PedsHIV\DICOM2nift\7000\MPGRAGE)

Set the id to be the subject number

Click convert; this will create subfolders for each series; for the T1 (MPRAGE), if there are two series, just use the first one.