Yes please use the HCP pipelines for myelin mapping.

Peace,

Matt.

On 6/19/15, 4:17 AM, "Donna Dierker" <do...@brainvis.wustl.edu> wrote:

>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:
>
>http://www.humanconnectome.org/documentation/HCP-pipelines/
>
>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:
>
>http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs
>_LR/Output
>
>(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.
>
>Donna
>
>
>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(they¹re 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
>>thanŠ .
>> 
>>  
>> 
>> I¹d appreciate any help and instructions.
>> 
>>  
>> 
>> Thanks,
>> 
>> 
>> Xara
>> 
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>
>
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