What operations beyond smoothing do you need? There is wb_command -cifti-smoothing.
Peace, Matt. From: Nicola Toschi <[email protected]<mailto:[email protected]>> Date: Wednesday, March 29, 2017 at 9:09 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere Hi Matt, thank you for your quick answer! That makes sense. I would like to do some spatial operations on the sphere that exploit spatial neighborhood information (e.g. even simple smoothing or filtering on the 2D surface), and have these operations be consistent across subjects. What would be the best way to go about this do you think? Incorporate the exact vertex locations for each subject anyway, or ignore them and (somehow) just use the fact that vertex n has the same neuroanatomical meaning in every subject? Thanks again, Nicola On 03/29/2017 04:02 PM, Glasser, Matthew wrote: We don¹t recommend using the ft_ tools with MRI data. Instead use ciftiopen/ciftisave/ciftisavereset: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ item 2B As for your other question, the vertex indices have neuroanatomical correspondence across subjects, but that often does not equate to having the same 3D coordinates (as volumetric registration is not able to align cortical areas across subjects). Peace, Matt. On 3/29/17, 8:41 AM, "[email protected] on behalf of Nicola Toschi"<mailto:[email protected]> <[email protected] on behalf of [email protected]><mailto:[email protected][email protected]> wrote: Dear List, I am trying to do some postprocessing on myelin and thickness maps (164k versions) contained in the MNINonLinear Directory of the Structural dataset (e.g. ${subject}.corrThickness_MSMAll.164k_fs_LR.dscalar.nii and ${subject}.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii). I thought these data would all be in the same atlas space across subjects, hence I was expecting to find the same vertex coordinates for all subjects. Instead, when reading the data into matlab ( 'ft_cifti_read' and gifti') every subject seems to have their own distinct vertex locations. Also, the spherical gifti surfaces appear to be sampled at different coordinates across subjects. Can I assume that, nonetheless, anatomical correspondence is preserved across subjects? Could I, for example, take the vertex locations from ${subject}.R.sphere.164k_fs_LR.surf.gii, associate the scalar values in ${subject}.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii to each vertex, interpolate on the sphere and assume that I can superimpose the results of this procedure across subjects? Thanks very much in advance! Nicola _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]>http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
