This pages describes how to manually get started with the REST toolbox, used for analyzing resting state fMRI (rsfMRI).
Pediatric HIV example
Software:
- 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.
Convert raw data to nifti
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.
