On Sep 1, 2017, at 9:09 AM, Harwell, John <[email protected]<mailto:[email protected]>> wrote:
It appears that my response on Tuesday did not go through, perhaps due to a change in my email address. John Begin forwarded message: From: "Harwell, John" <[email protected]<mailto:[email protected]>> Subject: Re: [caret-users] strange patches on grey surface? Date: August 29, 2017 at 9:41:22 AM CDT To: "Caret, SureFit, and SuMS software users" <[email protected]<mailto:[email protected]>> Hello, It may be a problem with some triangles incorrectly oriented. While viewing the left hemisphere, select these two menu items: * Surface Menu : Topology : Orient Tiles Consistently * Surface Menu : Normals : Generate Normals If it fixes the problem: * File Menu : Manage Files * On the Manage Loaded Files Dialog, save the modified topology file. John On Aug 29, 2017, at 7:05 AM, Alle Meije Wink <[email protected]<mailto:[email protected]>> 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-FIDUCIAL_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-FIDUCIAL_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-FIDUCIAL_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_left.png><caret_right.png>_______________________________________________ caret-users mailing list [email protected]<mailto:[email protected]> http://brainvis.wustl.edu/mailman/listinfo/caret-users
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