Alignment of skull-stripped T1s on hybrid DTI/pCASL MRI datasets

Greetings AFNI experts,

I have an alignment related issue that you might be able to help with:

I have skull-stripped T1 anatomical datasets that I need to align on top of hybrid DTI/pCASL datasets. Both the T1 and DTI/pCASL datasets have been collected in the same scan session:

T1: 1mm isotropic voxels (256x256x256 voxels)

Hybrid DTI/pCASL: 3.5mmx3.5mmx8.0mm (64x63x12 voxels) The one shown is an M0 image,

I can get a relatively, maybe sort of OK alignment if I do the following:

  1. Resample the Hybrid DTI/pCASL images to the T1 resolution
    3dresample -master ${s}_freesurfer_brain.nii.gz -prefix IMG_PLD2000_M0_RS.nii.gz -input IMG_PLD2000_M0.nii

  2. Align using and pretending the DTI/pCASL dataset is EPI -anat ${s}_freesurfer_brain.nii.gz -anat_has_skull no -epi IMG_PLD2000_M0_RS.nii.gz
    -epi_strip None -anat2epi -epi_base 0 -partial_coverage -volreg off -tshift off -suffix _AL_m0_RS.nii.gz

The output is depicted in the animated gif below (image shows the TI overlaid on top of the DTI/pCASL image after alignment):

The alignment is not totally horrible but I was wondering if there is anyway this can be improved. I can share my data if this will help,

Thank you in advance for your help,


That looks okay. It’s pretty rough in the DTI/pCASL dataset. You might try visualization with edges. You could try the nmi cost function to see if that comes out with something better.


Thank you for the quick response. The nmi cost function in combination with -big_move worked significantly better. Still not quite there but this might be the best we can do given the quality of the DTI/pCASL dataset. Thank you for your help,