Dear Dr Greve, Kindly, I wanted to know why "mri_coreg" apples smoothing during registration. e.g.
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
Are there any effects on the accuracy of smoothing if I turn off this default feature (specifically in pet surfer pipeline).
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --no-smooth
Thank you for any clarification John
I don't think that is turned on by default. There is smoothing of the NMI historgrams, but that is unrelated
On 08/21/2017 12:07 PM, John Anderson wrote:
Dear Dr Greve, Kindly, I wanted to know why "mri_coreg" apples smoothing during registration. e.g.
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
Are there any effects on the accuracy of smoothing if I turn off this default feature (specifically in pet surfer pipeline).
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --no-smooth
Thank you for any clarification John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Actually, it is on by default (thanks to Emma for pointing it out). The smoothing helps to blur anatomical differences which reduces the chance that it will get stuck in a local minimum. It will usually only smooth the reference, and only if it is high res; this can help the reference look a little more like the moveable. In the end, I don't think it makes much of a difference except to make it a little more robust.
On 08/21/2017 03:52 PM, Douglas N Greve wrote:
I don't think that is turned on by default. There is smoothing of the NMI historgrams, but that is unrelated
On 08/21/2017 12:07 PM, John Anderson wrote:
Dear Dr Greve, Kindly, I wanted to know why "mri_coreg" apples smoothing during registration. e.g.
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
Are there any effects on the accuracy of smoothing if I turn off this default feature (specifically in pet surfer pipeline).
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --no-smooth
Thank you for any clarification John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Actually thank you for me as well for such a nice question! ;-) This great response makes sense. Thank you very much Dr Greve for the follow up
-------- Original Message -------- Subject: Re: [Freesurfer] mri_coreg Local Time: August 23, 2017 6:49 PM UTC Time: August 23, 2017 10:49 PM From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu
Actually, it is on by default (thanks to Emma for pointing it out). The smoothing helps to blur anatomical differences which reduces the chance that it will get stuck in a local minimum. It will usually only smooth the reference, and only if it is high res; this can help the reference look a little more like the moveable. In the end, I don"t think it makes much of a difference except to make it a little more robust.
On 08/21/2017 03:52 PM, Douglas N Greve wrote:
I don"t think that is turned on by default. There is smoothing of the NMI historgrams, but that is unrelated
On 08/21/2017 12:07 PM, John Anderson wrote:
Dear Dr Greve, Kindly, I wanted to know why "mri_coreg" apples smoothing during registration. e.g.
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
Are there any effects on the accuracy of smoothing if I turn off this default feature (specifically in pet surfer pipeline).
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --no-smooth
Thank you for any clarification John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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