afni.nimh.nih.gov

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 align_epi_anat.py and pretending the DTI/pCASL dataset is EPI
align_epi_anat.py -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,

Valentinos