[Freesurfer] co-registration between slab of DTI image

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Hi Freesurfer experts,

I'm writing to ask about coregistration between a thin oblique coronal slab of DTI image ( only 15 slices) and a cubic 1x1x1 voxel size anatomical image (volume size is 256x256x256), with additional whole brain low-resolution DTI to assist registration. The codes I use are as attached:

I have few concerns: 1) the input oblique coronal slab of DWI image does not have header information, should it be better if I input the DWI slab in RAS coordinates (axial volume)?

2) Should I zero-fill the DWI slab to match the volume of T1.mgz? I already did that because it won't start to calculate the cost function between the thin DWI slab and anatomical image if I don't zero-fill. However, I feel like the cost function cannot make sense of the fact that the zeros are already outside the region of interest.

3) Should I use --init-fsl /--init-spm in this case? Neither of these two worked. Is there a better optimization function recommended?

I have been using fsl flirt function 2 step registration (from DWI slab to whole brain DWI; From whole brain DWI to whole brain anatomical image) to do the registration. But I don't think it's the best way.

For freesurfer bbregister, I have been trying to change things here and there, but the co-registration does not work well. Do you suggest to look at any parameter particularly based on this scenario?

Thank you for your help,

Yixin

Note that isoDWI111_256_axial.nii is the slab of DWI image EPI_iso111_256_axial.nii is the whole brain DWI image [The freesurfer reconstruction is performed before all these]

bbregister --s 30426 --mov isoDWI111_256_axial.nii --*int* EPI_iso111_256_axial.nii --init-fsl --reg xform_freesurfer.dat --dti

tkregister2 --reg xform_freesurfer.dat --mov isoDWI111_axial.nii

mri_vol2vol --reg xform_freesurfer.dat --mov isoDWI111_axial.nii --fstarg --o isoDWI111-*in*-anat.mgh

mri_convert isoDWI111-*in*-anat.mgh isoDWI111_reg.nii