We still don't have a SPM8 version, if that's really your question. ;-) SPM5 is what I would use, in your shoes.
If your functionals are in MNI space, as you say they are, then you're good. When you say "hdr" I assume that's a NIFTI hdr/img pair, and not an Analyze volume, because you're using SPM8, which I'm guessing outputs NIFTI by default. Your question about the space if valid: If you mapped volume to Caret, and used a currently loaded coord file, you'd need to be sure it was a coord like *SPM5*coord -- not *711-2*coord, which is possibly what is in that TEMPLATE spec. But because you mapped to Spec File with Atlas, *and chose SPM5* as the space for your PALS surface, Caret mapped your volume to a coord in your Caret distribution directory (e.g., $CARET_HOME/data_files/fmri_mapping_files/*PALS*SPM5*coord). Once it is mapped to a metric, you can view it on any surface in correspondence with the mapping surface (e.g., any space fiducial coord, inflated, very inflated, spherical, flat). So you should be good. When in doubt, I fish avg152T1.nii out of my FSL/SPM distribution; open it as an anatomy file in Caret; overlay my functional volume on it; and turn on my surface outline (D/C: Volume Surface Outline or something like that -- very last page selection). You might have to fish CARET_HOME/data_files/fmri_mapping_files out of your distribution directory, if it's not already in your spec file. This is the surface that needs to align with your functional. On Jul 12, 2012, at 8:19 AM, atesh koul wrote: > > Dear all, > > I am very new to caret ( and to the list of course). So please excuse me for > asking a question that has been debated a number of times on the list. > > All I want is to know if the procedure that I am using for mapping my > functional images from SPM8 (spm_t images) ( in MNI space) to PALS atlas : > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730, is correct or not. What > i am doing is the following (based on the sep06 caret tutorial on the web > http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/tutorials/Caret_Tutorial_5.5.html > ) : (and please correct me if there is anything wrong there) > > 1. Opening the spec file: > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec > 2. Renaming it to a different name. > 3. Using Map Volume(s) to Surface(s), using metric data. > 4. Selecting my .hdr images and then using the option Map to Spec File with > Atlas. > 5. Selecting my newly named spec file and using space as spm5 and atlas as > the PALS atlas for left and right. > 6. saving the metric files and using metric enclosing algorithm. > 7. For visualisation, I open the spec file. load the file and in D/C I use > overlay/underlay data type as metric. > 8. For threshold, I use the metric settings and user threshold. > > I want to confirm if the 'atlas and SPM5 space' options take care of the > registration (and I dont need to register my functionals or structurals to > caret atlas). In other words, what space is > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730 in? and is it the same as > for SPM8? > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
