Thank you Donna, Tobias, Mateus!! Both methods worked! Cheers, Gene
Eugene Tunik, PhD, PT Dept. of Physical Therapy, NYU http://homepages.nyu.edu/~et38/ ----- Original Message ----- From: Tobias Egner <[EMAIL PROTECTED]> Date: Wednesday, April 11, 2007 11:11 am Subject: Re: [caret-users] mapping functional data from SPM5 To: "Caret, SureFit, and SuMS software users" <caret-users@brainvis.wustl.edu> > 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 > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users
