PS: the fit of a sine and cosine to wedge/disk data (the classical retinotopic mapping) can be done with SPM by simply putting them into a design matrix. Amplutide and phase can then be derived from the beta images. These amplitude/phase images can then be turned into flat maps using Caret.
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
Room B.01.1.03
Mail : Huispost B01.206, P.O. Box 85500
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609
Fax : +31 (0)88 7555443
E-mail : [log in to unmask]
Web : http://www.neuromri.nl/people/bas-neggers
: http://www.brainsciencetools.com (CEO)
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________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Gabor Oederland [[log in to unmask]]
Sent: Thursday, August 09, 2012 3:43 PM
To: [log in to unmask]
Subject: Re: [SPM] ¦^Ī`”GRe:_[SPM]_¦^Ī`”GRe:_[SPM]_¦^Ī`”GRe:_[SPM]_How_to_create_Subject-Wise_Anatomical_ROI
Dear Ce,
there are several labs out there that provide stimuli for retinotopic analysis:
http://white.stanford.edu/Retinotopy
http://sampendu.wordpress.com/retinotopy-tutorial/
You will need Matlab and Psychophysics toolbox though.
Note that probably you won't be able to analyze the acquired data with SPM. Basically, you will have to reconstruct the surface of the cortex, map the fMRI data onto this surface and then analyze the data. This might be done e.g. with Brainvoyager ( http://support.brainvoyager.com/functional-analysis-statistics/99-retinotopic-mapping/221-users-guide-retinotopic-mapping-of-early-visual-areas.html ) or Freesurfer/FSL.
As you state, you only have experience with SPM so far. In this case, maybe Vistalab tools might be the best choice. You can do the preprocessing (realignment) in SPM and then switch to these tools. ITKGray allows a manual/partly automatic segmentation into grey and white matter ( http://white.stanford.edu/newlm/index.php/ItkGray ), the analysis is carried out with mrVistar (see http://white.stanford.edu/newlm/index.php/Retinotopy_Tutorial and http://www.alivelearn.net/?p=532 ).
In any case, it might be good to have someone around in the lab who has experience with these tools, be it Brainvoyager/Freesurfer or Vista tools.
Hope this helps,
Gabor
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