Jimmy Shen

"collapse_nii_scan" is used to integrate multiple single-volume NIfTI or ANALYZE files into one multiple-volume NIfTI file. In your case, if you want to concatenate two 4D NIfTI images into one 4D NIfTI images, you should apply "expand_nii_scan" to your both 4D images. All volumes must be in the same folder, and make sure the file name is correctly renamed (i.e. from 001~999 instead of 1~999). Then, apply "collapse_nii_scan" to all those expanded volumes in the specific folder, and you will get a concatenated 4D NIfTI image file.

Received the image, and it is a special RGB data type one. The nii.img ranges from 0 to 1 as usual, but the output value needs to be scaled by (glmax-glmin)+glmin.

Sure Mark. You need a reference image by the way, so you can see what will happen before and after you apply the transformation matrix. Here's the example:

1. Download "avg152T1_RL_nifti.nii" from NIfTI site. I use it as reference image.

2. View how the reference image looks like: nii=load_nii('avg152T1_RL_nifti.nii');
view_nii(nii);

3. Assume that I have a Transformation Matrix, which will let the reference image turn 30 degree counter-clockwise on XY plane, here will be the matrix: T=[cos(pi/6) -sin(pi/6) 0; sin(pi/6) cos(pi/6) 0; 0 0 1];

4. Get old_xyz from reference image: rl=load_untouch_nii('avg152T1_RL_nifti.nii');
old_xyz=[rl.hdr.hist.srow_x(1:3);rl.hdr.hist.srow_y(1:3);rl.hdr.hist.srow_z(1:3)];

5. Apply your transformation matrix, and save new_xyz into a new image: new_xyz=T*old_xyz; rl.hdr.hist.srow_x(1:3)=new_xyz(1,:); rl.hdr.hist.srow_y(1:3)=new_xyz(2,:); rl.hdr.hist.srow_z(1:3)=new_xyz(3,:); save_untouch_nii(rl, 'rl30.nii'); Now you already have the "rl30.nii", which is a transformed NIfTI image can be used anywhere.

6. In order to view this image using my toolbox, you need to reslice it: reslice_nii('rl30.nii', 'rl30b.nii'); Now, you can load and view the rotated image: rl30b=load_nii('rl30b.nii'); view_nii(rl30b);

Hopefully this answers your questions.

This is great. I replaced a hacked solution of my own that worked terribly with this in literally less that 5 minutes.

"collapse_nii_scan" is used to integrate multiple single-volume NIfTI or ANALYZE files into one multiple-volume NIfTI file. In your case, if you want to concatenate two 4D NIfTI images into one 4D NIfTI images, you should apply "expand_nii_scan" to your both 4D images. All volumes must be in the same folder, and make sure the file name is correctly renamed (i.e. from 001~999 instead of 1~999). Then, apply "collapse_nii_scan" to all those expanded volumes in the specific folder, and you will get a concatenated 4D NIfTI image file.