[Homer-users] Probabilistic Spatial Resgistration
TSUZUKI Daisuke
tsuzuki at jichi.ac.jp
Mon Feb 18 00:55:27 EST 2013
Hi Maria,
If you already install SPM and use it to normalize the MRI,
I recommend you to try the Matlab script provided by John.
It's the best, simplest and straight-forward way to normalize scalp positions.
http://www-personal.umich.edu/~nichols/JohnsGems2.html#Gem5
There are several methods about projection.
If you want to step forward to the details,
Okamoto and Dan, 2005 and Fekete et al., 2011 are helpful.
http://www.sciencedirect.com/science/article/pii/S1053811905000509
http://www.sciencedirect.com/science/article/pii/S1053811911003478
As a part of AtlasViewerGUI, the script named "ProjectionBI.m" is
included in "HOMER2/PACKAGES/AtlasViewerGUI/AAL/" directory.
This script was dedicated for balloon inflation method.
You can try it.
best,
From: Maria Arredondo <mmarre at umich.edu>
Subject: Re: [Homer-users] Probabilistic Spatial Resgistration
Date: Mon, 18 Feb 2013 00:02:52 -0500
Message-ID: <CAALEjc3413_jUuSrLKUq2H5rkKJSqhTsWX8T-WiGn1gj-7RcpA at mail.gmail.com>
> Hi all,
> To further extend this thread...
> I was wondering if anyone knows how to (or what program to use) to get
> reliable MNI coordinates when using a MRI scan.
> We scanned someone in the MRI using Vitamin E capsules on our cap, but
> currently we are unsure on how to convert the Vitamin E capsules to MNI
> coordinates. What program do you use to normalize and reliably project down
> into the brain the capsules? And how do you do it?
> Any suggestions are greatly appreciated!
> Thank you,
> -Maria
>
> On Mon, Feb 4, 2013 at 6:56 PM, Simone Cutini <simone.cutini at unipd.it> wrote:
>
> Hi Drew,
> you might also check the Münster T2T-Converter: http://
> wwwneuro03.uni-muenster.de/ger/t2tconv/
> Basically, it allows to obtain the MNI coordinates from 10-20 measurements
> (and viceversa).
> This is the link to the 3D app: http://wwwneuro03.uni-muenster.de/ger/
> t2tconv/conv3d.html
> Note that the results are slightly different from those observed in other
> studies on cranio-cerebral correlation.
>
> Simone
>
> Hi Austin,
>
> Thanks for your reply. I had indeed seen those slides from Ippeida
> Dan, but had glazed over the MNI table -- Thanks! I guess it would be
> fairly straight forward to put together a spreadsheet that computes
> 10-20 based on distance measurements.
>
> Cheers,
> Drew
>
> On Mon, Feb 4, 2013 at 11:57 AM, austin1 <astoudenmire at earthlink.net>
> wrote:
>
> Drew
>
>
>
> Dunno if you've seen this site:
>
> http://www.jichi.ac.jp/brainlab/download/fNIRS_Course_Dan.pdf
>
> but it might help some.
>
> Also, to compute 10-20 sites from distances (nasion-inion, etc.),
> it would just be a matter of percents from one to the other.
>
> Then the reference above gives a chart on one of the slides that
> shows 10-20 to MNI conversion.
>
> Is this something on the order of what you're looking for?
>
>
>
> Austin
>
> -----Original Message-----
> From: Drew Halliday
> Sent: Feb 1, 2013 5:07 PM
> To: homer-users at nmr.mgh.harvard.edu
> Subject: [Homer-users] Probabilistic Spatial Resgistration
>
> Hello NIRS community,
>
>
>
> Has anyone successfully used gross anatomical landmarks (e.g.,
> nasion, inion, left and right preauriculars) to computer
> probabilistic spatial registration using either Homer 2, or
> another program (e.g., fNRI Tools from Ippedia Dan’s group)?
> My understanding is that this can be done without MRI or 3D
> Digitizer data, however the disconnect for me is in computing
> 10-20 or MNI coordinates based simply on distances from
> nasion-inion, left-right preauriculars, and other combinations
> of distances between these landmarks.
>
>
>
> As the AltasViewer GUI in Homer 2 is not yet available, I have
> been using fNRI Tools, and to a lesser extent NIRS_SPM. An
> ‘origin’ and ‘others’ spreadsheet (.csv) are called during
> this process, however these spreadsheets contain x, y and z
> axis coordinates, presumably computed using either 3D
> digitizer data, MRI scans, or gross anatomical measurements.
>
>
>
> Does anyone know how to use a probe geometry file, combined
> with gross anatomical measurements, and produce said origin
> and others spreadsheets? All thoughts are welcomed!
>
>
>
> Thanks,
>
> Drew
>
> _______________________________________________
> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>
> 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.
>
> _______________________________________________
> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>
> 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.
>
> --
>
> Simone Cutini, PhD, Post-doctoral Research Fellow
> Department of General Psychology, University of Padova
> Via Venezia 8, 35131, Padova, Italy
> Tel: +39.049.8276528
> Fax: +39.049.8276600
> My Profile on Mendeley
>
> _______________________________________________
> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>
> 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.
>
> --
> Maria M. Arredondo
> Doctoral Student, Developmental Psychology
> University of Michigan
> 530 Church Street, 2036 East Hall
> Ann Arbor, MI 48109-1043
> Office: 734-936-3188
>
-TSUZUKI Daisuke-
|
| Postdoctoral Fellow |
| Functional Brain Science Lab |
| Center for Development of Advanced Medical Technology |
| Jichi Medical University |
| 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan |
| E-mail: tsuzuki at jichi.ac.jp |
| |
| 'Don't forget to think about what the intelligence is.'
More information about the Homer-users
mailing list