Dear experts,

I ran into an issue running mri_vol2vol after running bbregister using freesurfer 8.

Running the same commands in freesurfer 7.4.1 worked well. bbregister worked in both versions, while mri_vol2vol (8.0.0) resulted in the following error:

INFO: This REGISTER_DAT transform is valid only for volumes between  COR types with c_(r,a,s) = 0.

[...]

INFO: using NIfTI-1 sform (sform_code=2)

error: File exists

error: LTAchangeType: src geometry must be valid

Running version 7.4.1 mri_vol2vol using the .dat file generated with bbregister version 8.0.0 worked as well.

The commands:

# bbregister, where fs8 is the freesurfer directory of the subject (SUBJECTS_DIR has been set to 'structural_dir', in which fs8 is located)

reg_file="$out_dir/diff2str.dat"

bbregister --s fs8 --mov "$b0" --reg "$reg_file" --fslmat "${reg_file%.dat}.mat" --dti

# mri_vol2vol cmd below, working in version 7.4.1, but not in version 8.0.0

# with mov being a map of diffusion metrics in the same space as b0 here

mri_vol2vol \

        --mov "$mov" \ 

        --targ "$structural_dir/fs8/mri/T1.mgz" \

        --o "$output" \

        --no-save-reg --reg "$reg_file"

I also tried the following prior to mri_vol2vol, which did not help: mri_convert -rl "$b0" -rt nearest "$my_mov" "$my_mov_modified"

I encountered the same issue when running mri_vol2vol and bbregister with the identical input as --mov.

Might there be a bug in version 8's mri_vol2vol, or am I missing something?

Thank you for your help!

Best,

Felix

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