Hi 

My nii gz file for my MRI head scans for some reason are in a peculiar sequence  ie they do not follow on from one another 
Is there anyway to change the slice sequence so that it follows the MRI head sequence?

Thanks

This question is underspecified. Are you trying to reorder the 2D slices in a 3D volume, or the 3D volumes in a 4D time series? Why ais the image order scrambled - what is the source of these images and how were they converted (e.g. did you convert them from DICOM to NIfTI using dcm2niix)? I suspect a combination of fslroi and fslmerge can solve your issue, but it might be easier to fix it at the source.

> Hi Chris
>
So I am trying to reorder the 2D slices in a 3D volume
The source was DICOM files converted to Nifti
I can’t quite understand why the image order is scrambled - I’ve tried to
re-convert them to no avail
Is there any other bits of info that may help?
Thanks

>

Hi Chris

They are corrupt at the source so I fear I will have to rearrange the 2D images to create a 3D volume
Ive tried to reconvert the DICOM to nifti but no luck

Any idea's on how this can be done?

You could use fslsplit and fslmerge.

Alternatively, you could write a Python script using nibabel.