I understand that the map I see is in fact the myelin smooting something. So, ine the spec file, when I go to metric > open my metric file, I have a Choose Column to load window but no column has been loaded, and when I click ok, I receive the same error messag:
Error PDHCEM_Conte69_LEFT_midthickness_164k_fs_LR_7_May_2014_14_58_48.metric: contains a different number of nodes than Conte69.L.midthickness.164k_fs_LR.coord.gii Audrey-Anne Dubé Candidate au PhD R/I neuropsychologie Université de Montréal On Wed, May 7, 2014 at 2:52 PM, Audrey-Anne Dubé <[email protected]>wrote: > Ok I see an overlay! I didn't know I had to use Scene. > So that's good! But the problem now is that I the overlay is not related > to my statistical data, as you can see with the screen shot of my file in > Mango vs in Caret. > > > Audrey-Anne Dubé > Candidate au PhD R/I neuropsychologie > Université de Montréal > > > On Wed, May 7, 2014 at 2:20 PM, Audrey-Anne Dubé <[email protected] > > wrote: > >> Hi, >> >> My volume is in Tal space. Is this a problem? >> >> Audrey-Anne Dubé >> Candidate au PhD R/I neuropsychologie >> Université de Montréal >> >> >> On Wed, May 7, 2014 at 11:30 AM, Donna Dierker >> <[email protected]>wrote: >> >>> 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 >>> >> >> >
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