8.4. Using NIFTI data in AFNI

8.4.1. Overview

The TL;DR of this section is that it is easy to use NIFTI data in AFNI processing:

  1. Nearly all AFNI programs use NIFTI and BRIK/HEAD file formats interchangeably.

  2. All volume-processing programs accept NIFTIs as inputs—just use them directly.

  3. For most AFNI programs, you can just include .nii or .nii.gz on the output filename to output a NIFTI volume.

  4. If you do need to convert to/from NIFTI, that is easy to do with 3dcopy or several other programs.


8.4.2. Input NIFTI datasets to AFNI programs

Simply put, wherever you input a volumetric dataset to an AFNI program, you can just provide a NIFTI volume. That is, programs read in NIFTI or BRIK/HEAD datasets equivalently.

This applies to afni_proc.py, 3dttest++, 3dcalc, and basically every volumetric-processing program (e.g., see here and here). For example:

  • Create a mask:

    3dAutomask                                                             \
    -prefix  MASK                                                      \
    DSET.nii.gz

  • Multiply two datasets (one or both inputs could be NIFTI here):

    3dcalc                                                                 \
    -a       DSET_A.nii.gz                                             \
    -b       DSET_B+orig.HEAD                                          \
    -expr    'a*b'                                                     \
    -prefix  DSET_OUT

  • Calculate voxelwise statistics:

    3dTstat                                                                \
    -median                                                            \
    -prefix  OUTPUT_MED                                                \
    DSET_4D.nii.gz

... and so very many more.

8.4.3. Output NIFTI datasets from AFNI programs

For the vast majority of AFNI programs that output a volumetric dataset, whenever you specify the output name, simply put ``.nii`` or ``.nii.gz`` on the end of it, and the output will be in NIFTI format. There are also a couple programs that have a separate option used to specify having NIFTI format. For example:

  • Create a mask:

    3dAutomask                                                             \
    -prefix  MASK.nii.gz                                               \
    DSET.nii.gz

  • Multiply two datasets (one or both inputs could be NIFTI here):

    3dcalc                                                                 \
    -a       DSET_A.nii.gz                                             \
    -b       DSET_B+orig.HEAD                                          \
    -expr    'a*b'                                                     \
    -prefix  DSET_OUT.nii

  • Calculate voxelwise statistics:

    3dTstat                                                                \
    -median                                                            \
    -prefix  OUTPUT_MED.nii.gz                                         \
    DSET_4D.nii.gz

  • Threshold a continuous-valued dataset and output ROI maps, where each ROI is inflated a bit but in a way to not spread far into white matter (NB: this program requires the -nifti option to output volumes in NIFTI format):

    3dROIMaker                                                             \
    -inset             CORR_VALUES.nii                                 \
    -thresh            0.6                                             \
    -volthr            100                                             \
    -inflate           2                                               \
    -wm_skel           WM_T1+orig.                                     \
    -skel_stop_strict                                                  \
    -prefix            ROI_MAP                                         \
    -nifti

... and many, many more. If you don’t add one of those file extensions, then AFNI programs by default will output the volume(s) in BRIK/HEAD. But you could just convert that to NIFTI directly then, anyways.

Note that a couple “higher level” wrapper programs do not output NIFTIs directly. The FMRI pipeline-generating program afni_proc.py is one of these. Once can just convert the desired volumes of interest to NIFTI volumes directly.

8.4.4. Convert BRIK/HEAD -> NIFTI

There are many ways to do this, which are fairly equivalent. We mention a few approaches, because they might have additionally useful functionality at the same time.

3dcopy. This is the simplest approach:

3dcopy DSET DSET.nii.gz

3dAFNItoNIFTI. Another simple approach with short syntax, but one that will adapt any BRIK/HEAD file with multiple scale factors to having just one for the NIFTI file (and there are a few other options regarding header adjustments):

3dAFNItoNIFTI -prefix DSET.nii.gz DSET

3dcalc. This might be useful if you also want to specify the data type, for example, but that is not necessary:

3dcalc -a DSET -expr 'a' -prefix DSET.nii -datum float

... and can also add subbrick/subvolume selectors:

3dcalc -a DSET"[0..4,7,10-14]" -expr 'a' -prefix DSET.nii -datum float

3dTcat. If you want to combine multiple volumes to a single NIFTI:

3dTcat -prefix DSET_COMBO.nii.gz DSET1+orig DSET2+orig DSET3+orig ...

3dresample. If you want to alter header information (that is assumed to be correct at present):

3dresample -prefix DSET_NEW.nii.gz -orient RAI -input DSET+tlrc

3dresample                                                             \
    -prefix DSET_NEW.nii.gz                                            \
    -master MNI152_2009_template_SSW.nii.gz                            \
    -input  DSET+tlrc

... and several others.

8.4.5. Convert NIFTI -> BRIK/HEAD

Pretty much each of the programs in the Convert BRIK/HEAD -> NIFTI section apply here, and you would simply not put an extension on the output dataset name. So, for example:

3dcopy. This is the simplest approach:

3dcopy DSET.nii DSET

... etc.