Hi Xara,

Because you are in the enviable position of having high res T1 AND T2, you may 
be able to use the Human Connectome Project pipelines on your data, rather than 
this (older generation) caret-based myelin mapping script:


This also has the advantage of writing output files in workbench formats, 
rather than older caret formats.  I have a hunch that Matt Glasser will point 
you in that direction (he is probably at OHBM conference or on his way home).

I confess I am not as familiar with this script as Matt is, but from what I 
read at the link you sent, it appears the maps are on the native mesh, rather 
than 164k.  And I don't see myelin represented in the list of 
freesurfer_to_fs_LR output files here:


(These were independent efforts going on at roughly the same time.)

You may already have considered the HCP pipeline route, but if not, it is worth 
a look -- you've got the T2's at the right res, which is often a hitch.  I 
suspect myelin maps on 164k won't be your only benefit.


On Jun 19, 2015, at 8:58 AM, "Shams, Z." <z.sh...@donders.ru.nl> wrote:

> Dear users,
> I just started working with Caret for creating myelin maps. I used HCP 
> imaging protocols for data acquisition, both T1 and T2 data have the voxel 
> size of 0.7mm isotropic.
> I followed the instructions in 
> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping.
> Actually I managed to display the four outputs, but some parts of the maps 
> are missing when overlaying on a surface(they’re not complete maps: either 
> raw or corrected myelin maps).
> Another problem is that I used the freesurfer to fs LR script to convert all 
> my freesurfer files to the 164k_fs_LR mesh,
> but when I try  to show the myelin maps on e.g. very-inflated 164k fs LR, It 
> fails with the error of containing a different number of nodes than… .
> I’d appreciate any help and instructions.
> Thanks,
> Xara
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> caret-users@brainvis.wustl.edu
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