Another thought occurred to me: If you select a 32k version of the Conte69 atlas as your spec file, then you'll get an error when you try to open the 164k vertex metric file. I'm sure there is a way to downsample the metric file, and there are also mapping features in Workbench's wb_command, if you want to map directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in caret5.
On May 7, 2014, at 9:58 AM, Donna Dierker <[email protected]> wrote: > 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
