Could you zip up the Output spec file and its contents and upload the zip file
here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Also, do you already have a spec file loaded when you select Attributes: Map
volume to surface?
If so, try this without loading a spec file first.
On May 7, 2014, at 2:09 PM, Audrey-Anne Dubé wrote:
> 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
> 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
> 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
> 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 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
> > 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
> >> 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 SPHER
