Re: [HCP-Users] Custom parcellation for HCP data

Hi Tim, Have you had a chance to look into this issue? Thanks, Simon On 18 October 2016 at 15:15, Simon Baker wrote: > Hi Tim, > > Using FreeView, I loaded HCP subject 101410's MNINonLinear/T1w_restore_brain, > MNINonLinear/aparc+aseg, and

Re: [HCP-Users] Custom parcellation for HCP data

You might want to compare them to the T1 in an example subject (and perhaps also volume surface outline for pial), to see what is really going on. The pial surfaces of the two hemispheres shouldn't overlap outside the medial wall. Are you mapping to the structural volume resolution, or to the

Re: [HCP-Users] Custom parcellation for HCP data

Note that this command just makes the left hemisphere take precedence - you said the overlap was in medial wall, which is more of an artifact of processing than a structure of importance, so this should be fine. The surfaces shouldn't have any overlap on real structures, so ribbon constrained

Re: [HCP-Users] Custom parcellation for HCP data

Assuming that your label values don't have any overlap (each integer uniquely identifies not only the area but also the hemisphere), you can do the math part with wb_command -volume-math: wb_command -volume-math 'L + (L == 0) * R' ${Subject}.custom_raw.nii.gz -var L ${Subject}.L.custom.nii -var

Re: [HCP-Users] Custom parcellation for HCP data

:* Wednesday, December 16, 2015 4:25 PM > *To:* Jennifer Elam > *Cc:* hcp-users@humanconnectome.org > > *Subject:* Re: [HCP-Users] Custom parcellation for HCP data > > > > Hi Jenn, > > > > Thanks for your advice about the structural extended preprocessed data > packa

Re: [HCP-Users] Custom parcellation for HCP data

: Simon Baker [mailto:simonteba...@gmail.com] Sent: Wednesday, December 16, 2015 4:25 PM To: Jennifer Elam Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Custom parcellation for HCP data Hi Jenn, Thanks for your advice about the structural extended preprocessed data packages

Re: [HCP-Users] Custom parcellation for HCP data

www.humanconnectome.org From: hcp-users-boun...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Simon Baker Sent: Sunday, November 15, 2015 5:41 PM To: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Custom parcellation for HCP data Thanks for your

Re: [HCP-Users] Custom parcellation for HCP data

on Baker <simonteba...@gmail.com> > Date: Sunday, October 18, 2015 8:16 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Custom parcellation for HCP data > > Hi all, > > We want to create a custom parcellation

Re: [HCP-Users] Custom parcellation for HCP data

cp-users@humanconnectome.org>>, Simon Baker <simonteba...@gmail.com<mailto:simonteba...@gmail.com>> Subject: Re: [HCP-Users] Custom parcellation for HCP data Additionally, if you generate a cortex-only parcellation, you shouldn't need to put it into a volume to use it with the HC

[HCP-Users] Custom parcellation for HCP data

Hi all, We want to create a custom parcellation for use with the connectome project data. However, we have not been able to achieve accurate spatial alignment between the random parcellation volume and the T1w volume. Specifically, there appears to be an "offset," possibly due to a mismatch