Hi Audrey-Anne, Erin and I tried to do that, but you can't see the menu picks very clearly in the video:
https://www.youtube.com/watch?v=jED8sg9szdU But here are the steps: Download conte69 atlas: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293720&archive_name=Conte69_atlas_v2.LR.164k_fs_LR.c5.zip Unpack and cd to the Conte69_164k_fs_LR.c5 directory. Launch caret5. Cancel when spec file dialog comes up. Attributes: Map volume to surface Data mapping type: Metric; Next Add volumes from disk; select volume in MNI space; next Map to spec file with atlas Note: If you don't see this, then your caret installation is incomplete or confused about its parent directory. Launch from command line. Output spec file: select Conte69_atlas-v2.L.164k_fs_LR.c5.spec Space: FNIRT Atlas: Conte69 Map LEFT midthickness... Next Accept default metric filename Mapping Algorithm: Enclosing and interpolated are the most popular Next Close when Summary appears File: Open Spec File: Conte69_atlas-v2.L.164k_fs_LR.c5.spec Load scenes Double-click first scene (Conte69 midthickness and inflated...) Toolbar: Spec: Metric: map_data_0_Conte69... Erase all existing columns Toolbar: D/C: Page Selection: Overlay/underlay Surface Primary overlay Data type metric metric You should see it. Donna On May 6, 2014, at 7:36 PM, Audrey-Anne Dubé <[email protected]> wrote: > 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 > > _______________________________________________ > 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
