Dear Freesurfer experts,
I have two questions regarding preproc-sess:
1) What is the default algorithm that does the functional-anatomical registration? And is there any way to change the default to other types of registration methods?
2) If I do not want to normalize to template, i.e. I want to keep the image in native space, should I be using -noreg or -noinorm?
Thanks, Jiahe
1) bbregister ("Accurate and robust brain image alignment using...") 2) We don't typically resample - most analyses are done in native space by default
cheers Bruce
On Thu, 31 Aug 2017, Jiahe Zhang wrote:
Dear Freesurfer experts, I have two questions regarding preproc-sess:
- What is the default algorithm that does the functional-anatomical registration? And is there any
way to change the default to other types of registration methods?
- If I do not want to normalize to template, i.e. I want to keep the image in native space, should
I be using -noreg or -noinorm?
Thanks, Jiahe
-- Jiahe ZhangPh.D. Candidate Department of Psychology Northeastern University 617-373-4789
On 08/31/2017 11:47 AM, Jiahe Zhang wrote:
Dear Freesurfer experts,
I have two questions regarding preproc-sess:
- What is the default algorithm that does the functional-anatomical
registration? And is there any way to change the default to other types of registration methods?
it uses bbregister. There is no easy way to change it
- If I do not want to normalize to template, i.e. I want to keep the
image in native space, should I be using -noreg or -noinorm?
Use the -per-session option and dont specify a hemisphere or mni305
Thanks, Jiahe
-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Bruce and Doug! Follow-up questions: which anatomical volume does bbregister register the functional to? Also, is there any need to reorient the functional image before preprocessing?
On Tue, Sep 5, 2017 at 11:34 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 08/31/2017 11:47 AM, Jiahe Zhang wrote:
Dear Freesurfer experts,
I have two questions regarding preproc-sess:
- What is the default algorithm that does the functional-anatomical
registration? And is there any way to change the default to other types of registration methods?
it uses bbregister. There is no easy way to change it
- If I do not want to normalize to template, i.e. I want to keep the
image in native space, should I be using -noreg or -noinorm?
Use the -per-session option and dont specify a hemisphere or mni305
Thanks, Jiahe
-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Technically, it does not use an anatomical volume but rather the surfaces derived from the conformed volume (so the registration will be good for any conformed volume). No need to reorient the functionals as long as the header info about the head orientation is correct.
On 10/6/17 5:29 PM, Jiahe Zhang wrote:
Thanks Bruce and Doug! Follow-up questions: which anatomical volume does bbregister register the functional to? Also, is there any need to reorient the functional image before preprocessing?
On Tue, Sep 5, 2017 at 11:34 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 08/31/2017 11:47 AM, Jiahe Zhang wrote: > Dear Freesurfer experts, > > I have two questions regarding preproc-sess: > > 1) What is the default algorithm that does the functional-anatomical > registration? And is there any way to change the default to other > types of registration methods? it uses bbregister. There is no easy way to change it > > 2) If I do not want to normalize to template, i.e. I want to keep the > image in native space, should I be using -noreg or -noinorm? Use the -per-session option and dont specify a hemisphere or mni305 > > Thanks, > Jiahe > > > -- > Jiahe Zhang > Ph.D. Candidate > Department of Psychology > Northeastern University > 617-373-4789 <tel:617-373-4789> > > > _______________________________________________ > 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> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ 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> 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 <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.-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649 tel:%28617%29%20373-2649
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Jiahe Zhang