That looks like a problem with the coordinates or possibly with the topology of what you loaded as the left surfaces. I'm not really sure how that would happen. You can open the "Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.LEFT.73730.spec" file itself (part of the caret-data package, I expect) and just display the surfaces, and see if that has the same issue.
Lengthy side note: Caret5 is older software, no longer maintained. Connectome Workbench is its successor, and can do many of the same things, with more intuitive controls: http://www.humanconnectome.org/software/connectome-workbench However, it does not have options in the GUI for the same kind of processing, as we have shifted almost entirely to the command line and scripts for that purpose (much easier to tweak a pipeline script then recompile the software). The basic command needed for this type of operation is "wb_command -volume-to-surface-mapping", which will map one nifti volume file to one surface, which we use to map single-individual data to the surfaces of that same individual, which gives us significant gains by bypassing the volume registration problem entirely. It can be used, with a moderate amount of scripting and some additional commands, to do what the caret5 function you want to use does (map a group volume file to many subjects' surfaces, then average). Now for the bad news: The average errors of nonlinear volume registration in cortex are rather high due to folding variability, larger than the fMRI resolutions we now use (2mm for 3T using multiband), and will be much worse for linear volume registration such as FLIRT. The fMRI mapping method you are using is largely intended as a workaround for simply viewing legacy group volume data, where the individual data is not available for reprocessing with better methods. We recommend against using volume-based group analysis of cortex in new studies. See here for an example of the specificity and reproducibility we can get with surface-based group analysis (2 independent groups of subjects, click on the image to enlarge): https://balsa.wustl.edu/WDpX Tim On Tue, Aug 29, 2017 at 7:05 AM, Alle Meije Wink <a.m.w...@gmail.com> wrote: > Mapping a functional volume onto the caret surfaces made with FLIRT, I get > some strange black/white coloured patches in only the left hemisphere. > > My computer has Debian 9 (Stretch) and I have installed caret and > caret-data from the NeuroDebian repository. > I follow the instructions of http://brainvis.wustl.edu/wiki > /index.php/Caret:Operations/MapVolumeToSurface: > > From main window: > -- menu -> attributes -> map volume(s) to surface(s) > -- data mapping type -> metric (functional) or surface shape data > -- volume selection -> add volumes from disk -> *<my own nii.gz file, > resolution 4x4x4 mm^3> (thresholded to only show negative clusters)* > -- spec file and surface selection -> map to spec file -> > Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.LEFT.73730.spec > spec file > -> topology file -> Human.sphere_6.LEFT.HEM.73730.topo *(no others > possible)* > fiducual > coordinate files -> select all coord files (12x) > map to spec file -> > Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.RIGHT.73730.spec > spec file > -> topology file -> Human.sphere_6.RIGHT.HEM.73730.topo *(no others > possible)* > fiducual > coordinate files -> select all coord files (12x) > -- data file naming -> surface family -> Human.PALS_B12.LR.MULTI-FIDUCI > AL_FLIRT_fMRI-MAPPER.B1-12.LEFT.73730.spec (12 coord files) > data file -> > *map_data_2_29_Aug_2017_12_33_32.metric* > surface family -> > Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.RIGHT.73730.spec > (12 coord files) > data file -> > *map_data_3_29_Aug_2017_12_35_25.metric* > -- mapping algorithm -> metric_enclosing_voxel > > Back to main window: > -- menu -> file -> open spec file > -- specification file: Human.PALS_B12.LR.MULTI-FIDUCI > AL_FLIRT_fMRI-MAPPER.B1-12.LEFT.73730.spec > coordination files -> select all > -- metric file: *map_data_0_29_Aug_2017_12_33_32.metric* > -> window captured as caret_left.png > > Back to main window: > -- menu -> file -> open spec file > -- specification file: Human.PALS_B12.LR.MULTI-FIDUCI > AL_FLIRT_fMRI-MAPPER.B1-12.RIGHT.73730.spec > coordination files -> select all > -- metric file: *map_data_1_29_Aug_2017_12_35_25.metric* > -> window captured as caret_right.png > > Now the right hemisphere looks brilliant (both with and without the > functional values mapped in) but the left hemisphere has these dark to > light patches all over the brain surface. And they appear in all models, > for left, and for non in the right hemishere. > > Is there a setting that can make the left hemispere mappings 'clean' as > well? > Or should I use a different .spec file? All the examples on the internet > use *Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec* but I can > only find the left and right hemispheres separately. > > Many thanks for your help! > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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