Generally I thought you could only directly subsample the regular icosahedron spheres (e.g. 2562, 10242, 40962, 163492). The native mesh sphere isn’t going to be amenable to that sort of thing as it is very irregular (varying numbers of neighbors per
vertex, varying vertex spacing, etc). One
Probably need to specify your probtrackx2 command lines, but both rigid alignment to MNI space and nonlinear alignment are available in the ${StudyFolder}/${Subject}/T1w and ${StudyFolder}/${Subject}/MNINonLinear locations respectively.
Peace,
Matt.
From: Archer, Derek B
Hi Matt,
So to get the diffusion data into the standard space, which files are relevant
under the MNINonLinear folder? Sorry for the confusion.
Derek
From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Monday, May 18, 2015 3:15 PM
To: Archer,Derek B; hcp-users@humanconnectome.org
We dont do it that way. Use probtrackx2 flags --xfm=${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz and --invxfm=${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to bring seeds from standard space into structural
space and the results from structural
Hi Matt,
I'm looking at the preprocessed data that I downloaded from ConnectomeDB, and I
am not seeing the MNINonLinear folder. Under the subject folder, there are
the following folders:
.xdlm
release-notes
T1w
Do I need to download from elsewhere to get the nonlinear alignment?
Thanks,
You also need to download the structural data.
Peace,
Matt.
From: Archer, Derek B arche...@ad.ufl.edu
Date: Monday, May 18, 2015 at 2:12 PM
To: Matt Glasser glass...@wusm.wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: RE: [HCP-Users] Minimal
I would check that your SE field map has the same geometry and echo spacing as your SBRef. Also I would post some examples of what looks wrong to you in your processing.
Peace,
Matt.
From: Juan Sanchez sanch...@nyspi.columbia.edu
Date: Monday, May 18, 2015 at 3:21 PM
To:
Back on this other question, wb_command indeed does not do decimation of
the remove vertices from existing topology variety. The usual way to do
surface downsampling with wb_command is to generate a new sphere with the
desired number of vertices (and highly regular topology/spacing), and then
hi HCP,
we are trying to do tractography using FSL and HCP data. i have some questions
-- i suspect they have been answered already, but couldn't find those answers:
1. is there a file containing the grayordinate coordinates in the diffusion
space for a particular subject, both subcortical
