Dear Donna, It is not a read-only issue since the spec files are modified when I do the mapping. Here is exactly what I did:
1. open CARET v5.65 2. Attributes > Map volume(s) to surface(s) 3. chose Metric for Data mapping type 4. Enable entry of volume threshold 5. Add volumes from disk --> selected my ALE map, which is a nifti image, in Talairach format 6. Entered the volume thresholding in the pop-up window (positive: 0.028; negative: 0.00) 7. Map to spec file with Atlas 8. select in fmri_mapping_files > Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you suggested 9. Space : FNIRT; Atlas: Conte69 Map LEFT midthickness (164k_LR nodes) 10. idem 8 and 9, but with RIGHT 11. renamed by data files (L and R) 12. Mapping algorith: METRIC_ENCLOSING_VOXEL 13. ok (or next), heard a "bip" like there was an error, but the summary shows 14. Close 15. Open spec file > Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec 16. check my metric file (please see joint image) > load 17. Got this error message Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_5_May_2014_11_13_13.metric: contains a different number of nodes than Conte69.L.midthickness.164k_fs_LR.coord.gii Pressed ok 18. The brain image is displayed, but without my data on it Can you see if I did something wrong? Thanks very much Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, Apr 30, 2014 at 3:22 PM, Donna Dierker <[email protected]>wrote: > Hi Audrey, > > Hmmm. I wonder if this might be because the spec file you name below is > part of the Caret distribution, and it might be read-only. In fact, it's a > good idea for it to be read-only. The files under data_files are intended > to be used by Caret without risk of users writing their analysis files > there. Is this spec file under $CARET_HOME/data_files or has it been > copied from there? And is the directory and spec file writeable? > > There are better choices for other visualization specs, e.g., like those > in this tutorial spec: > > http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/CARET_TUTORIAL_SEPT06.zip > login pub > password download > > Also, depending on the constraints of your meta-analysis, you might > consider moving from the PALS atlas to the Conte69 atlas: > > http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas > > > Donna > > > On Apr 30, 2014, at 1:19 PM, Audrey-Anne Dubé <[email protected]> > wrote: > > > Dear Caret users, > > > > I want to map my meta-analysis results on an PALS surface. So I tried to > map my ALE map (nifti format) to a surface atlas using this spec file > > > Human.PALS_B12.LR.MULTI-FIDUCIAL_711-2C_fMRI-MAPPER.B1-12.RIGHT.align2.73730.spec > > > > I got this error message: > > Error PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: Error > PDHCEM_Mapped_to_PALS.RIGHT.73730.metric: contains a different number of > nodes than > Human_Buck_Case12.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align2.73730.coord > > > > I cannot figure how to resolve this problem. Help would be greatly > appreciated! > > > > Thank! > > > > Audrey-Anne Dubé > > Candidate au PhD R/I neuropsychologie > > Université de Montréal > > _______________________________________________ > > 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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