On Sep 1, 2017, at 9:09 AM, Harwell, John 
<john.harw...@email.wustl.edu<mailto:john.harw...@email.wustl.edu>> 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" 
<john.harw...@email.wustl.edu<mailto:john.harw...@email.wustl.edu>>
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" 
<caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu>>

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 
<a.m.w...@gmail.com<mailto: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-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>_______________________________________________
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