AFNI MNI and FSL nifti space


I downloaded a striatum mask from FSL. It is in .nii form. I am trying to use it with one of my AFNI datasets that is in MNI. But if I open the two datasets side by side the don’t seem to line up. Specifically, in my MNI dataset, the part I am interested in seems to be in the striatum (caudate; confirmed by using the whereami function) but this point is completely outside the mask. I have a screenshot that can illustrate. Is there any way I can check or change the alignment?

Thanks a lot for any help!

Post the link for the mask dataset, and I’ll try to figure it out.

Thank you! It is a mask that is included with FSL - here are the details:

I can also give you the masks themselves if you tell me where to upload / send it?

I’ll PM you with upload or email the masks. Compressed, they should be tiny attachments.

perfect! thank you


I uploaded the files - did you receive it?

Thank you so much for your time!



Everything looks okay to me. The mask fits over the MNI_152_T1+tlrc template in the expected areas. The cluster output does overlap the left and right caudates in two of the clusters. A third cluster is away from those. whereami’s output suggests the atlas region of the focus point, but that doesn’t mean it is the only area involved or even that specific region necessarly. The overlap output from the Clusterize plugin WamI button shows that too with the overlap of each of the three clusters with various atlases. You can get similar output on the command line with whereami (this command is actually run by the clusterize plugin. In your case, this was the whereami command (looking for at least a 20 voxel cluster and no threshold) :

3dclust -1Dformat -nosum -1dindex 0 -1tindex 0 -dxyz=1 -savemask Clust_mask 1.01 20 redo_mask_AD_TD_4_3_t_mask+tlrc.HEAD
whereami -omask ./Clust_mask+tlrc.HEAD

Okay. That makes sense. Thank you!