Trouble saving concatenated nifti's in matlab

1

I am trying to concatenate two nifti files together in matlab. To do this, I open both nifti files, concatenate the volumes along the last dimension, then save with niftiwrite(volume,‘filename’). However, upon trying to save with niftiwrite, I am repeatedly getting this error:

Error using images.internal.nifti.niftiImage/writeHeader

Cannot open file for writing header.

I can’t find anything about it online, on this forum, or on matlab’s forum. Any ideas?

Best,
Hank

2

Hi @hankghgold,

Does filename include .nii.gz? That may be required. If the file name argument includes the full path, you should make sure that full directory tree exists. But I do not use MATLAB - this can be also be done pretty handily in python with Nibabel/Nilearn if you are not tied to MATLAB.

Best,
Steven

3

Hello Steven,

Thank you! I’ll try that out and get back to you. I’m not fully tied to matlab, but i know my PI prefers this done in matlab if possible.

4

Including .gz didn’t work :confused:

5

Hi @hankghgold,

To clarify, did you include .nii.gz or just .gz? Also what is the contents of volume ?

Best,
Steven

6

Hi Steven,

.nii.gz, and the contents of volume are 4d images.

Best,
Hank

7

Can you be more specific about what you mean by an image? It looks like it only expects numeric 3/4d data arrays for the main argument (that is, not image objects or anything extra like metadata), is that what you have?