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You could try affine first and initialize the deformable registration with
that. Something like:
mri_synthmorph -m affine fa.nii.gz template.nii.gz -t affine.txt
mri_synthmorph -m deform -i affine.txt fa.nii.gz template.nii.gz -o
fa_in_MNI.nii.gz
Alternatively, assuming your T1 is aligned with the FA map, you can run the
above on the T1, save the warp with `-t warp.nii.gz` in the second call, and
apply it to the FA map:
mri_warp_convert -g t1.nii.gz --inras warp.nii.gz --outm3z warp.m3z
mri_convert -at warp.m3z fa.nii.gz fa_in_MNI.nii.gz
________________________________________
From: John Anderson <jb19790...@gmail.com>
Sent: Friday, September 1, 2023 13:43
To: Freesurfer support list; Hoffmann, Malte,PhD
Subject: Re: [Freesurfer] mri_synthmorph
External Email - Use Caution
Dear Malte
Thank you so much. I've tried both rigid and affine transformations, and I've
attached a snapshot that shows how the CC doesn't fully overlap with the
template. I'm using a high-quality DTI image and am wondering if incorporating
a T1 image would help improve the registration. I'm not sure how to apply a
two-step registration, if that's even possible, using mri_synthmorph. Thanks
for your guidance.
Best,
John
On Fri, Sep 1, 2023 at 1:27 PM Hoffmann, Malte,PhD
<mhoffm...@mgh.harvard.edu<mailto:mhoffm...@mgh.harvard.edu>> wrote:
External Email - Use Caution
Hi John,
Currently, the default transformation model is "deform". Could you check if
"affine" yields a better result?
mri_synthmorph -m affine fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz
Cheers,
Malte
________________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of John Anderson <jb19790...@gmail.com<mailto:jb19790...@gmail.com>>
Sent: Friday, September 1, 2023 12:45
To: Freesurfer support list
Subject: [Freesurfer] mri_synthmorph
External Email - Use Caution
Dear Freesurfer experts,
I processed DTI data using dt_recon, and I want to register FA images to the
standard MNI152 space. However, after running the command
mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,
the registration is not accurate. I'm not sure what I've done wrong. Thank you
for any guidance.
sincerely
J
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