Dear Doug & others
The FSL page on fa to freesurfer registration ( http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html) contain info that uses tkregister2.
To determine freesurfer_to_fa space registration file, do we need to go through the freesurfer_to_struc and then struc_to_fa rooutine given in fsl pages.?
I wonder if the registration can be done using the bbregister currently.
If that is the case how to get the fsl-type registration file? tkregister2 had an option for this but it is not working with bbregister
Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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I get a file-not-found to that link, so I can't check it out. But, yes, you should just be able to use bbregister passing it the low-b as the template (or whatever you used at the target for motion correction). and specifying --bold or --t2.
doug
Lena Palaniyappan wrote:
Dear Doug & others
The FSL page on fa to freesurfer registration ( http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html) http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html%29 contain info that uses tkregister2.
To determine freesurfer_to_fa space registration file, do we need to go through the freesurfer_to_struc and then struc_to_fa rooutine given in fsl pages.?
I wonder if the registration can be done using the bbregister currently.
If that is the case how to get the fsl-type registration file? tkregister2 had an option for this but it is not working with bbregister
Cheers Lena _______________________________________________________ *Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Hi Doug,
This reminds me: in the dt_recon script, when bbregister is used, the gradient descent tolerance is changed (the command line includes --tol1d 1e-3 ).
I was just wondering why this happens.
Thanks! Mike
On Tue, Jan 25, 2011 at 1:31 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
I get a file-not-found to that link, so I can't check it out. But, yes, you should just be able to use bbregister passing it the low-b as the template (or whatever you used at the target for motion correction). and specifying --bold or --t2.
doug
Lena Palaniyappan wrote:
Dear Doug & others
The FSL page on fa to freesurfer registration ( http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html) http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html%29 contain info that uses tkregister2.
To determine freesurfer_to_fa space registration file, do we need to go through the freesurfer_to_struc and then struc_to_fa rooutine given in fsl pages.?
I wonder if the registration can be done using the bbregister currently.
If that is the case how to get the fsl-type registration file? tkregister2 had an option for this but it is not working with bbregister
Cheers Lena _______________________________________________________ *Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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It should not. I've already made the change to our code base. You can just delete that spec in your version of the script if you want. Thanks for the note!
doug
Michael Waskom wrote:
Hi Doug,
This reminds me: in the dt_recon script, when bbregister is used, the gradient descent tolerance is changed (the command line includes --tol1d 1e-3 ).
I was just wondering why this happens.
Thanks! Mike
On Tue, Jan 25, 2011 at 1:31 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I get a file-not-found to that link, so I can't check it out. But, yes, you should just be able to use bbregister passing it the low-b as the template (or whatever you used at the target for motion correction). and specifying --bold or --t2. doug Lena Palaniyappan wrote: > Dear Doug & others > > > The FSL page on fa to freesurfer registration ( > http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html) > <http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html%29> contain info > that uses tkregister2. > > > > To determine freesurfer_to_fa space registration file, do we need to > go through the freesurfer_to_struc and then struc_to_fa rooutine given > in fsl pages.? > > I wonder if the registration can be done using the bbregister currently. > > If that is the case how to get the fsl-type registration file? > tkregister2 had an option for this but it is not working with bbregister > > Cheers > Lena > _______________________________________________________ > *Lena Palaniyappan > *Clinical Lecturer & Honorary StR | Division of Psychiatry ( > University of Nottingham) > South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please send it back to me, and immediately delete > it. Please do not use, copy or disclose the information contained in > this message or in any attachment. Any views or opinions expressed by > the author of this email do not necessarily reflect the views of the > University of Nottingham. > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Douglas N Greve -
Lena Palaniyappan -
Michael Waskom