[caret-users] mapping functional data from SPM5

[Eugene Tunik]

Hi Donna,
I have a quick question about a caret problem.
I installed v.5.51 on a new windows machine. (and the tutorial sept 06 toolbox).
I just want to map functional volume to surface so I do the following:

1) load spec file (in mapping procedures->PALs for fmri mapping

2) attributes-=> map to surface...and go through the whole deal of loading my image file (SPM space).

When the whole thing is done, and I click D/C, the metric icon doesn't become active so I cannot overlay anything.

(The same functional works fine on a different machine that has an older installation of caret).

Any suggestions?
Thanks and best,
Gene




Eugene Tunik, PhD, PT
Dept. of Physical Therapy, NYU
http://homepages.nyu.edu/~et38/

----- Original Message -----
From: Donna Dierker <donna at brainvis.wustl.edu>
Date: Wednesday, April 11, 2007 9:28 am
Subject: Re: [caret-users] mapping functional data from SPM5
To: "Caret, SureFit, and SuMS software users" <caret-users at brainvis.wustl.edu>


> Hi Gene,
> 
> It might take you 15 minutes to wade through this whole thread, but it 
> 
> will resonate:
> 
> http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01088.html
> 
> Here are the highlights:
> 
> * Caret only reads NIFTI files that are a single file with the ".nii" 
> 
> extension. The next release of Caret will be able to read NIFTI files 
> 
> that are in an Analyze hdr/img pair.  Caret still reads the files as 
> if 
> they were Analyze, but without the SPM99/SPM2-style "originator" info 
> in 
> the .hdr, it's clueless about the location of the origin.
> 
> * Use Volume: Edit volume attributes to set the origin to -90,-126,-72.
> 
> * When opening the functional volume in Caret, select the "Volume is 
> an 
> SPM2 Volume with Right on Left" if your volume is stored in a 
> left-handed coordinate system (aka radilogical or right on left -- see 
> 
> http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q15).  If you need 
> 
> to map several functional volumes and want to use the caret_map_fmri 
> command line utility, then you'll probably need to convert your 
> volumes 
> to *.nii, AFNI, or SPM2-style .hdr.
> 
> Donna
> 
> On 04/11/2007 07:50 AM, Eugene Tunik wrote:
> > Dear all,
> > I am mapping a contrast image (the spmT.hdr/img) that is output in SPM5.
> > However, Caret is not mapping it to the fiducial. This works fine 
> using an spmT image output from SPM2.
> >
> > Is there something special about the SPM5 output that makes it 
> incompatible with caret?
> >
> > Any suggestions are appreciated.
> >
> > Best,
> > Gene
> >
> >
> >
> >
> > Eugene Tunik, PhD, PT
> > Dept. of Physical Therapy, NYU
> > http://homepages.nyu.edu/~et38/
> > _______________________________________________
> > caret-users mailing list
> > caret-users at brainvis.wustl.edu
> > http://pulvinar.wustl.edu/mailman/listinfo/caret-users
> >
> >   
> 
> 
> -- 
> Donna L. Dierker
> (Formerly Donna Hanlon; no change in marital status -- see 
> http://home.att.net/~donna.hanlon for details.)
> 
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