Convert nifti to fmr and change the orientations.

NII_to_FMR_orientation_fix.m

% Convert nifti to fmr and change the orientations.
% This scripts requires neuroelf.
%
% NOTES
% -----
% If you are getting erro about `Dyn3DToFMR`:
%    1. Clone the recent neuroelf version from <https://github.com/neuroelf/neuroelf-matlab> (this is written on 2020/04/28).
%    2. Copy `hdr_Dyn3DToFMR.m` file from neuroelf/_todo/@xff/private/ directory and paste in into neuroelf/@xff/private/ directory.
%    3. Comment out the following line fmrc.FirstDataSourceFile = hdrs.F; because otherwise it produces an error.
%    4. Add this modified neuroelf's path to your MATLAB.
%
% This should make the `Dyn3DToFMR` underfied error go away.

clear all; close all;

% Load
nii = xff('/path/to/file.nii');
fmr = nii.Dyn3DToFMR;
data = fmr.Slice.STCData;

% Flip or permute data (change fmr headers if permute)
data = flipdim(data,1);

% save
fmr.Slice.STCData = data;
fmr.SaveAs('/path/to/file_reorient.fmr')

Hi,
This looks exactly like what I need. However, I get an error when running it:

"mr = nii.Dyn3DToFMR;
Error using xff/subsref (line 202)
Field or method Dyn3DToFMR unknown for type HDR objects."

Is a specific way to call that function? The closest function I have is "hdr_Dyn3DToFMR", but that one also crashes.
Thank you!

Hello @ortiztudelaJ,

For some reason I did not receive any Github notification about this before and saw it now randomly.

What you need to do is to:

1. clone the recent neuroelf version from here
2. copy hdr_Dyn3DToFMR.m file from neuroelf/_todo/@xff/private/ directory and paste in into neuroelf/@xff/private/ directory.
3. Comment out the following line fmrc.FirstDataSourceFile = hdrs.F; because otherwise it produces an error.
4. Add this modified neuroelf's path to your MATLAB.

Now Dyn3DToFMR method will work.

I will add these instructions as comments in the script. Probably something has changed in the neuroelf over the years and this method became hidden away.