You didn't specify the format -- .nii or .hdr/.img. Try to write your volume as .nii and see how it maps. If you must use .hdr/.img (e.g., it really is SPM2 data), then use File: Open Data File: Volume Functional file to open the volume. Specify the data is right on left (checkbox on file open dialog, I believe). Then map loaded volume, rather than volume from disk.
> Hi Donna: > > The is Caret version 5. I used the same version with another set of data > analyzed on SPM5 and no problem, it is mostly as you expected, hemispheres > flipped, can I flip them back on caret using the same spmT files? > > Thank you! > > Soha > On Fri, Sep 4, 2009 at 3:21 PM, Donna Dierker > <[email protected]>wrote: > >> I'm not sure how old your Caret version is, but older versions of Caret >> couldn't read NIfTI files as .hdr/.img; you had to write them as .nii to >> get sensible results. I suspect the left is getting mapped to right and >> vice versa, because your Caret version isn't reading the NIfTI volume >> properly. >> >> If you're not using NIfTI, then fixing that is step 1. >> >> On 09/04/2009 01:28 PM, soha saleh wrote: >> > Dear Caret users: >> > >> > I am trying to import fMRI data from a group study analyzed using SPM2 >> > as a metric file so that I can view it on the PALS atlas. *However, >> > the activations are shown in the wrong anatomical place!* >> > >> > This is what I do to map the volume to surface and to open the spec >> file: >> > >> > Attributes\Map volumes to surface >> > data mapping type : metric >> > add volumes from disk : the spmT files Umt_Pmt_mask >> > map to spec with atlas: >> > Output spec file: select >> > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec from this >> > tutorial ( CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES) >> > Mapping Atlas: SPM2 >> > Atlas: >> > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec >> > Mapping algorithm: Metric enclosing voxel >> > >> > Now load spec file >> > file\open spec file : >> > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec >> > SPACE: SPM2 >> > category: atlas >> > species: human >> > subject: PALS-B12 >> > >> > select (Fiducial) and (Inflated) coordinates, and the metric file >> > created after I did map volume to surface. I convert metric to RGB, I >> > overlay the RGB data, and I have wrong activations. >> > >> > I attached a ppt. file that has 2 slides each showing the same spmT >> > file on either Caret or SPM2 result figure, both at threshold T=3. >> > >> > Between, I did the same procedure with data analyzed using SPM5 and >> > had no problem. >> > >> > I hope anybody can help, thanks in advance! >> > >> > Soha Saleh >> > phD candidate >> > Department of Biomedical Engineering >> > New Jersey Institute of Technology >> > [email protected] <mailto:[email protected]> >> > 1 (201) 951 0029 >> > >> > >> > >> > >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > 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 >> > _______________________________________________ > 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
