Gene, as Donna pointed out, you can alternatively use your SPM5 *.img and *.hdr files, but you will have to adjust the origin: Open them in Caret (select the "Volume is an SPM2 Volume with Right on Left") , then select Volume: Edit Volume and manually change the origins to -90, -126, -72. Once you have applied those parameters you should see the t-image roughly in the center of the Caret window. Save these changes to the image and then go through the standard steps for mapping volumes onto an atlas, but make sure you select the SPM2 space atlas. This worked fine for me.
Good luck, Tobias. On 4/11/07, Eugene Tunik <[EMAIL PROTECTED]> wrote:
Thank you Donna. So what I gather is that until the new version of Caret is released, I should just convert the paired-format NIFTI spmT's into the .nii format....Then the map to attributes should work, correct? Thanks, Gene Eugene Tunik, PhD, PT Dept. of Physical Therapy, NYU http://homepages.nyu.edu/~et38/ ----- Original Message ----- From: Donna Dierker <[EMAIL PROTECTED]> 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@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@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.) > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
-- Tobias Egner, Ph.D. Cognitive Neurology and Alzheimer's Disease Center Feinberg School of Medicine Northwestern University 320 East Superior, Searle 11 Chicago, IL 60611 Ph: (+1) 312 503 1749 Fax: (+1) 312 908 8789
