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" "$my_mov_modified" I encountered the same issue when running mri_vol2vol and bbregister with the identical input as --mov.
Might there be a bug in version 8's mri_vol2vol, or am I missing something?
Thank you for your help!
Best,
Felix
Try using -lta instead of --reg
On 7/5/2025 12:22 PM, Zahnert, Felix wrote:
Dear experts, I ran into an issue running mri_vol2vol after running bbregister using freesurfer 8. Running the same commands in freesurfer 7.4.1 worked well. bbregister worked in both versions, while mri_vol2vol (8.0.0) resulted in the following error:
INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. [...] INFO: using NIfTI-1 sform (sform_code=2) error: File exists error: LTAchangeType: src geometry must be valid
Running version 7.4.1 mri_vol2vol using the .dat file generated with bbregister version 8.0.0 worked as well.
The commands:
# bbregister, where fs8 is the freesurfer directory of the subject (SUBJECTS_DIR has been set to 'structural_dir', in which fs8 is located) reg_file="$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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That works, thank you! Best, Felix ________________________________ From: Douglas N. Greve dgreve@mgh.harvard.edu Sent: Sunday, July 6, 2025 6:30 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: mri_vol2vol bug in fs8.0.0?
Try using -lta instead of --reg
On 7/5/2025 12:22 PM, Zahnert, Felix wrote: 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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Zahnert, Felix