We don't have B0 fieldmap data, would I still be able to perform this correction? For preprocessing we ran eddy_openmp and dtifit. 

The helpdesk has added klawms to your sudo groups for access to the data. Please let me know if you need any more information. 

Thanks so much for your help,

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Sunday, April 25, 2021 10:39 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FA map registration to T1

Everything looks ok in the log file. Did you do an B0 distortion correction? Can you give me access to that data?

Log file is attached. 

Thank you,

Andrew

Andrew Russo

Clinical Research Coordinator 

Multiple Sclerosis Imaging Lab 

Massachusetts General Hospital 

149 13th Street | Boston, MA 02129 

617-726-7531

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Tuesday, April 20, 2021 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FA map registration to T1

 

can you send the bbr log file?

On 4/19/2021 2:29 PM, Russo, Andrew William wrote:

Hello FreeSurfer Developers, 

I am registering FA maps to T1 for a group of subjects with MS and in many cases the registration is poor for the anterior corpus callosum (attached), cerebellum, pons, and temporal lobe. I am using the following commands (FreeSurfer version 6.0):

bbregister \

    --dti \

    --reg diff2T1_reg.dat \

    --mov eddy_corrected_b0.nii.gz \

    --s subject_temp

mri_vol2vol \

    --mov dtifit_FA.nii.gz \

    --targ orig.mgz \

    --o FA2T1.nii.gz \

    --reg diff2T1_reg.dat

Do you have any suggestions for improving this registration? 

Thank you,
Andrew

Andrew Russo

Clinical Research Coordinator 

Multiple Sclerosis Imaging Lab 

Massachusetts General Hospital 

149 13th Street | Boston, MA 02129 

617-726-7531

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