Nifti

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Nifti files are used by FSL. With extension .nii or .nii.gz

Usages

Convert .nii <-> .nii.gz

nii.gz are simply gzipped .nii files, which are smaller in size. Sometimes you might want to convert between them. Simply run

gzip file.nii

to convert nii -> nii.gz; and

gunzip file.nii.gz

for nii.gz -> nii

Conversion

Dicom->Nifti

The most reliable dicom to nifti converter is dcm2nii, as it works with GE scanner headers correctly.

Orientation

It's important to check image orientation after file conversion.

fslswapdim will do this.

check header information with mrinfo (MRTrix) or mri_info.