I took a look at the data. It looks like pretty large B0 distortion to
me (just look at the eye balls). If you don't have a B0 map, then
there's not much you can do.
On 4/26/2021 8:29 AM, Russo, Andrew William wrote:
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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?
On 4/20/2021 10:34 AM, Russo, Andrew William wrote:
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-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 Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Tuesday, April 20, 2021 10:09 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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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