Please always check NIfTI_tools.pdf for detail descriptions and latest updates.

If you are confused by the Left / Right of an ANALYZE image, please read UseANALYZE.pdf.

You may also want to go through FAQ.pdf for practical solutions and real examples.

Basic Programs:

1. load_untouch_header_only.m: Load only the header section of NIfTI or ANALYZE file. The input file will be automatically detected. NIfTI structure will be returned for NIfTI file, and ANALYZE structure will be returned for ANALYZE file.

2. load_nii.m: Load N-Dimensional NIfTI file (where N can be from 3 to 7) or ANALYZE file (where N can be from 3 to 4), and apply header info (e.g. affine geometric transform, voxel intensity scaling, etc.) to the data. If your file has more than 3-Dimension (e.g. time series etc.), you can also specify a range to extract only 1 or several volumes.

3. save_nii.m: Save N-Dimensional NIfTI structure (where N can be from 3 to 7) that is loaded by "load_nii.m" or made by "make_nii.m" into a NIfTI file.

4. make_nii.m: Make N-Dimensional NIfTI structure (where N can be from 3 to 7) based on the N-Dimensional matrix and other optional parameters (e.g. voxel_size, origin, etc.). Using "save_nii" command, the NIfTI structure that is made by "make_nii" can be saved into a NIfTI file.

5. make_ana.m: Make 3D ANALYZE structure based on the 3D matrix and other optional parameters (e.g. voxel_size, origin, etc.). Using "save_untouch_nii" command, the ANALYZE structure that is made by "make_ana" can be saved into an ANALYZE file in order to be compatible with some ANALYZE only programs.

6. reslice_nii.m: Re-sample 3D (or 4D) NIfTI file, or ANALYZE file with affine matrix M in .mat file, and save the re-sampled data into a new NIfTI file. The program will base on the affine matrix, which is especially useful for oblique images with non-orthogonal rotation or shearing that cannot be loaded with "load_nii.m". You can also specify voxel_size, etc. It will not cause negative effect, as long as you remember not to do slice time correction after using "reslice_nii.m".

7. pad_nii.m: Pad the volume(s) in NIfTI structure from any of the six sides, while keeping the originator, voxel size, data type, and description unchanged. The program is especially useful after you use reslice_nii, since the new volume will most likely have different dimensions.

8. clip_nii.m: Clip the volume(s) in NIfTI structure from any of the six sides, while keeping the originator, voxel size, data type, and description unchanged. The program is especially useful after you use reslice_nii, since the new volume will most likely have different dimensions.

9. view_nii.m: View & Edit 3D (or 4D) NIfTI or ANALYZE structure that is loaded by "load_nii.m" or made by "make_nii.m". Activation map, ROI, etc. can be overlaid on top of a background image (see above picture). Plotted view can be embedded into your existing figure window. If you use it as an individual program, it can also edit the orientation and voxel value of the image, view volume histogram, and save the modified image.

10. load_untouch_nii.m: Load N-Dimensional NIfTI file (where N can be from 3 to 7) or ANALYZE file (where N can be from 3 to 4), but do not apply any changes that are indicated in the header. WARNING: Do not use "view_nii.m" to view the structure that is loaded by "load_untouch_nii.m".

11. save_untouch_nii.m: Save N-Dimensional NIfTI structure (where N can be from 3 to 7) or ANALYZE structure (where N can be from 3 to 4) that is loaded by "load_untouch_nii.m" or made by "make_ana.m" into a new NIfTI or ANALYZE file. If you do not modify the loaded dataset, the header and data in the new saved file should be the same as those in the original file.

Other Programs:

1. collapse_nii_scan.m: Integrate multiple single-scan NIfTI or ANALYZE files into a multiple-scan NIfTI file.

2. expand_nii_scan.m: Break a multiple-scan NIfTI file into multiple single-scan NIfTI files.

3. save_untouch_slice.m: Save back to the original image with a portion of slices that was loaded by load_untouch_nii. You can process those slices matrix in any way, as long as their dimension is not altered.

4. get_nii_frame.m: Return the number of time frames of a NIfTI file.

5. flip_lr.m: Flip NIfTI or ANALYZE file Left-Right along the plane across the originator, and save the L-R flipped data into a NIfTI file. WARNING: Please use this program with caution, although you can always flip it back.

6. load_nii_ext.m: Load header extension from a NIfTI file.

7. mat_into_hdr.m: Integrate affine matrix in old SPM .mat file into its .hdr header file. Thus, the ANALYZE file is converted into a NIfTI file with the updated .hdr header file.