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 <do...@brainvis.wustl.edu>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 <do...@brainvis.wustl.edu> > 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 <audreyanned...@gmail.com> > 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 <do...@brainvis.wustl.edu> > 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 <audreyanned...@gmail.com> > 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 < > audreyanned...@gmail.com> 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 < > do...@brainvis.wustl.edu> 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 < > audreyanned...@gmail.com> 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 > >>>> caret-users@brainvis.wustl.edu > >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >>> > >>> > >>> _______________________________________________ > >>> caret-users mailing list > >>> caret-users@brainvis.wustl.edu > >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >>> > >>> > >>> <Screen Shot 2014-05-05 at > 11.18.18.jpg>_______________________________________________ > >>> caret-users mailing list > >>> caret-users@brainvis.wustl.edu > >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> _______________________________________________ > >> caret-users mailing list > >> caret-users@brainvis.wustl.edu > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> _______________________________________________ > >> caret-users mailing list > >> caret-users@brainvis.wustl.edu > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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