Yes please use the HCP pipelines for myelin mapping. Peace,
Matt. On 6/19/15, 4:17 AM, "Donna Dierker" <[email protected]> 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." <[email protected]> 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 >>than . >> >> >> >> I¹d appreciate any help and instructions. >> >> >> >> Thanks, >> >> >> Xara >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > >_______________________________________________ >caret-users mailing list >[email protected] >http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
