The naming conventions are somewhat historical at this point and I would
probably do something clearer if I were to do it over:
${StudyFolder}/${Subject}/T1w/* ‹ Native volume space (i.e. undistorted
subject T1w rigidly aligned to MNI)
${StudyFolder}/${Subject}/MNINonLinear/* ‹ MNI volume space (T1w
nonlinearly volume registered to MNI)
${StudyFolder}/${Subject}/${VolumeSpace}/Native/* ‹ Native surface mesh
${StudyFolder}/${Subject}/${VolumeSpace}/fsaverage_LR32k/* ‹ 32k standard
mesh (2mm average vertex spacing‹used to make standard 2mm 91282
grayordiantes space)
There is also a higher resolution standard mesh in MNI volume space and
located in ${StudyFolder}/${Subject}/MNINonLinear/* at 164k (less than 1mm
average vertex spacing).
Spheres don¹t exist in a registered volume space, and we don¹t provide
multiple copies of files that would be the same. The native mesh
unregistered sphere is:
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.sphe
re.native.surf.gii
All of this is described in more detail in the HCP Minimal Preprocessing
Pipelines paper:
http://www.sciencedirect.com/science/article/pii/S1053811913005053
Peace,
Matt.
On 4/7/15, 2:43 PM, "Peter Savadjiev" <[email protected]> wrote:
>Hi,
>
>I am trying to understand the exact difference between FreeSurfer files
>in T1w/Native vs. those in MNINonLinear/Native, and any help would be
>much appreciated! Specifically, I'm trying to understand how the
>vertices in a surface in T1w/Native map to the vertices on the
>corresponding surface in MNINonLinear/Native.
>
>The HCP Manual
>http://www.humanconnectome.org/documentation/S500/HCP_S500+MEG2_Release_Re
>ference_Manual.pdf
>states on p. 72 that
>MNINonLinear/Native replicates some of the files in T1w/Native but
>contains additional files used during surface-based registration.
>
>However, when I compare for instance
>T1w/Native/117122.R.white.native.surf.gii
>and
>MNINonLinear/Native/117122.R.white.native.surf.gii
>I see that the vertex coordinates are different, i.e. the files are not
>simply replicates of each other. In which case, should I assume that the
>MNINonLinear/Native version of the files is not actually in Native
>space, but rather in MNI space maybe? In which case, I'm confused about
>the use of the word Native in naming the directory. Should I assume that
>files in MNINonLinear/Native have been rigidly transformed to the MNI
>space and are not in Native space?
>
>My other question is, other than a change in vertex coordinates, are
>there other changes in the surface itself, e.g. in topology or vertex
>ordering? Or can I assume that vertex #1 in
>T1w/Native/117122.R.white.native.surf.gii corresponds to vertex #1 in
>MNINonLinear/Native/117122.R.white.native.surf.gii, vertex #1000 in
>T1w/Native/117122.R.white.native.surf.gii corresponds to vertex #1000 in
>MNINonLinear/Native/117122.R.white.native.surf.gii and so on?
>
>The reason I'm asking these questions is that I would like to work with
>the sphere surface mesh file in Native space. But then, I was looking
>for the sphere surface file in
>T1w/Native/117122.R.sphere.native.surf.gii and did not find it, I only
>found MNINonLinear/Native/117122.R.sphere.native.surf.gii, and that's
>why I'm trying to understand the vertex correspondence between files in
>T1w/Native and MNINonLinear/Native.
>
>Thank you very much!
>
>Peter
>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.
>
>
>_______________________________________________
>HCP-Users mailing list
>[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.
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
