Hi Donna, As you suggested, I tried with the Conte69 atlas (164k and 74k), but same results. The metric file is recorded in the spec file, but the same error shows about different number of nodes.
Thanks for paying attention to my problem. Would it be possible for you to make an online demonstration, with a screen sharing or a screen cast tool? In this way, we may find a way to solve the issue faster. Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Tue, May 6, 2014 at 9:50 AM, Donna Dierker <[email protected]>wrote: > Audrey, > > I will look at this more closely later, but this is the step where you > should be downloading the Conte69 atlas and using one of its visualization > specs instead of this spec out of the distribution directory: > > > 8. select in fmri_mapping_files > > Human.Conte69.midthickness_FNIRT_fMRI-MAPPER.LEFT.164k_fs_LR.spec as you > suggested > > The Conte69 atlas is here: > > http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas > > I wonder if your writing to the fmri_mapping_files that are intended to be > read-only might cause trouble. > > Also, I would not expect to find a SPHERE or CMW configuration in that > fmri_mapping_files spec. > > Will look more at this later, but here are some hints as to what looks > amiss. > > Donna > > > On May 5, 2014, at 10:28 AM, Audrey-Anne Dubé <[email protected]> > wrote: > > > Here the attached image > > > > Audrey-Anne Dubé > > Candidate au PhD R/I neuropsychologie > > Université de Montréal > > > > > > On Mon, May 5, 2014 at 11:23 AM, Audrey-Anne Dubé < > [email protected]> wrote: > > 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 > > > > > > <Screen Shot 2014-05-05 at > 11.18.18.jpg>_______________________________________________ > > 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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