Re: [Freesurfer] BBRegistration with FSL topup

[Douglas N. Greve]

The vsm (voxel shift map) needs to be in the same voxel space as the 
fMRI (ie, it has to have the same voxel size, number of voxels, and the 
voxels must line up with the fMRI)


On 4/11/2024 8:11 PM, Gianluca Guglietti wrote:


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Hi,

I had a question as to how to integrate fsl's topup command for 
correcting B0 distortion with freesurfer's boundary-based 
registration. I am working with high-resolution epi data (0.8mm 
isotropic) with a reduced FOV and am trying to register it to an 
MP2RAGE structural scan that I've already run through free surfer's 
recon-all. When I use the BBR command it works perfectly fine but when 
I try to add the topup field map it fails, returning this error 
"MRIvol2surfVSM: vsm dimension mismatch 1".


the field map was generated using two reverse phase encoded SE-EPI 
volumes with the same resolution and field of view as the GE-EPI BOLD 
data I am trying to register.


Any advice would be greatly appreciated!

Best,

Gianluca

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[Freesurfer] BBRegistration with FSL topup

[Gianluca Guglietti]

External Email - Use Caution

Hi,

I had a question as to how to integrate fsl's topup command for correcting B0 
distortion with freesurfer's boundary-based registration. I am working with 
high-resolution epi data (0.8mm isotropic) with a reduced FOV and am trying to 
register it to an MP2RAGE structural scan that I've already run through free 
surfer's recon-all. When I use the BBR command it works perfectly fine but when 
I try to add the topup field map it fails, returning this error 
"MRIvol2surfVSM: vsm dimension mismatch 1".

the field map was generated using two reverse phase encoded SE-EPI volumes with 
the same resolution and field of view as the GE-EPI BOLD data I am trying to 
register.

Any advice would be greatly appreciated!

Best,

Gianluca
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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