Notes about imaging tool FSL

FSL is a famous tool for medical imaging analysis. Here are some notes.

(Note: Assume you are using ubuntu, and you use Debian repo to install fsl, which all the fsl softwares started with fsl5.0-“)

1. To open the FSL in terminal, type “fsl5.0-fsl”.

2. FSL only can view nii images, use dcm2nii to convert DICOM to nii.

(use software center to install dcm2nii)

3. Use FLIRT linear registration for image registration

4. 4D nii is a stack of 3D nii  files along time (time-series data).

5. fsl5.0-flirt for 3D registration (fsl5.0-mcflirt for 4D registration)

6. Do Skull removal before brain registration.

7. Choose image with higher resolution as reference