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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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?
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Tuesday, April 20, 2021 10:09 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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?
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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Russo, Andrew William