Imaging Data Formats

From BrainImagingCenter

Data collected from the scanner are in PAR/REC format and converted to SPM/ANALYZE using the DBIC's par_convert utility. Other supported formats include NIfTI and AFNI (BRIK+HEAD).

In addition to conversion from PAR/REC to ANALYZE, NIfTI & AFNI it is also possible to use command line tools to convert between formats.

• To convert between 3D analyze and NIfTI formats (note: you must run from the shell, not MATLAB):

$ fslchfiletype NIFTI output input
$ fslchfiletype ANALYZE output input

• To create a gzipped nifti file from a 3D analyze image, simply use:

$ fslchfiletype NIFTI_GZ output input

• To convert a series of 3D images (e.g. bold1_0001.img ... bold1_000n.img) to a single 4D NIfTI file:

$ fslmerge -t bold1 bold1*.img

• To convert a 4D NIfTI file to a series of 3D images:

$ fslsplit bold1 bold1_ -t

• Notes on using 4D fMRI volumes with SPM5/8.

John Ashbuner provides notes on using 4d volumes with SPM5/8.