How to crop nifti files

I know this may be a simple solution, but how does one crop a nifti file of a brain? I am trying to remove the skull and I’ve been stuck at this issue for quite some time. I have used segmentation wizard (or segmentation) module to highlight the regions I don’t want cropped, but cannot seem to figure out what module to use to actually cropt the rest out. I really appreciate all of the help!

If you already done the segmentations of the regions that you want to remove, install the Segment Editor Extra Effects extension and use mask volume function to save a version of your volume with just the brain. Then you can use the Crop Volume if you still want to remove the empty background.

If you need to remove the skull from MRI images, then you can use SwissSkullStripper extension. It removes the skull from the image completely automatically.

I forgot to mention that I am using rodent images, and SwissSkullStripper is probably human-based, correct?

Will the outcome of this process still be in nifti? Your method was great for cropping out the desired stuff, but I cannot seem to save it back as a nifti file again.

The skull stripper should work for any species, just provide your own template (a single image volume and a corresponding brain segmentation).

The result can be save in many formats, including nifti (you can choose file format in the save dialog).

You can save the masked volume in any format slicer supports (including Nifti). Just use the save as dialog box.


These files are multi-volume nifti and I am attaching a dropbox link of an example of my data.

So far, my steps include

1- MultiVolume Importer–>Select folder where .nii file in–>output node–>create new MRML MultiVolume–>click Import (Output node becomes a 200 frames NIfTI MultiVolume)
2. MultiVolume Explorer Module–>select input multivolume as 200 frames NIfTI MultiVolume (can click play)
3. Segment editor module w/ segment editor extra effects add-on installed–>segment portion I want
4. Mask Volume (within segment editor)–>save new dataset with only segmented region
5. Crop volume module–>apply (I am able to visualize the masked, cropped image exclusively.

The problem occurs because I cannot save the masked cropped image into a .nii file, as the only options are .nrrd or .nhdr format.

If you need to export multivolume as a .nii file, that functionality is not available. You can only save multivolumes as .nhdr/.nrrd.

Try the brain extraction tool in FSL?

Or FreeSurfer?