Thanks Donna for your prompt reply and sorry to trouble you again with this. If I understand correctly, I can use Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730 spec file (which is in MNI space) and use the atlas setting as SPM5 and since I used the option - mapped to spec file with atlas(SPM5), the spec is good to go with my MNI normalised functional images. Also I should check the same with avg152T1.nii from the SPM distribution.
Atesh On Fri, Jul 13, 2012 at 12:18 AM, Donna Dierker <[email protected]>wrote: > 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 > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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