Dear Tim,
Hi. Lots of thanks to your very detailed answer! :)
Yes, I agree with you that it would be better to do tractography in the subject
native volume space. And it is good to know that the MMP1.0 can be also used in
"T1w"-space surfaces. However, there is one existed problem that I cannot
figure out. The tfMRI outputs (e.g. tstat1.dtseries.nii) of the
"$Subject_3T_tfMRI_$TASK_analysis_s2.zip" are in the CIFTI grayordinates
standard space, with the directory of "MNINonlinear". There is no T1w folder
for the native cortical surface in the tfMRI s2 file.
To do tractography in native volume space, I suppose the surface ROIs should
also go back to the native surface. But with the only standardly registered
tfMRI grayordinate output, how should I change back?
Best regards,
Xinyang
At 2018-04-05 04:54:04, "Timothy Coalson" <tsc...@mst.edu> wrote:
Inline replies to some comments.
Tim
On Wed, Apr 4, 2018 at 7:38 AM, Xinyang Liu <xinyang_ie...@163.com> wrote:
Dear Matthew,
Thank you very much for your detailed explanation!
1. The current situation of our study is that, we used the HCP MMP1.0 atlas to
sample the tfMRI data in order to localize specific functional areas. Since the
HCP MMP1.0 is in the MNI space,
No, it isn't, because version 1.0 is a surface-only parcellation.
Surface-based labels or scalar data are not in any volume space, it is only the
geometry files (*.surf.gii) that have any coordinates in them at all. It is
also correct to use the MMP1.0 with "T1w"-space surfaces (MSMAll is
recommended).
we used
"$SUBJECT/MNINonLinear/fsaverage_LR32k/$SUBJECT.L.midthickness._MSMAll.32k_fs_LR.surf.gii"
to do the multiplication. Then I suppose the surface ROI to be acquired in the
MNI standard space, and therefore need to use the --xfm and --invxfm in
probtrackx2. Is my understanding correct?
As I understand it, tracking in subject native (T1w) volume space is strongly
recommended, because the nonlinear MNI warp could change the paths that
tractography takes to be something unrealistic. The T1w space is an
undistorted, rigid aligned version of the scanner space of the anatomical
images (and the T1w space diffusion data has had its vectors rotated to match
this rigid alignment), and thus the white matter is the same shape as it is in
the subject's head.
2. In this way, do the HCP data contain files that can be used in --xfm,
--invxfm and --seedref in surface prob-tracking?
3. In the FSL "surf2surf" format conversion from .func.gii to ASCII type
(.asc), is it correct to use
"$Subject/MNINonLinear/fsaverage_LR32k/${Subject}.R.white.32k_fs_LR.surf.gii"
as the input (-i) and the acquired "ROI.func.gii" as --value?
I haven't used this, I would say try it and see what happens. Maybe someone
else can tell you what they did.
Look forward to your kind guidance. Thanks a lot!
Best regards,
Xinyang
At 2018-04-04 18:44:25, "Glasser, Matthew" <glass...@wustl.edu> wrote:
1. Files in ${StudyFolder}/${Subject}/T1w are in subject’s physical space and
files in ${StudyFolder}/${Subject}/MNINonLinear are in MNI standard space.
Surfaces without MSMAll are registered with MSMSulc and surfaces with MSMAll
are registered with MSMAll. In general MSMAll will have better alignment of
cortical areas across subjects.
2. There is no native diffusion space, as this is unnecessary. Tracking
occurs subject’s physical space and you can use the surfaces in
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k with MSMAll if you don’t use
--xfm and --invxfm or those in
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k if you do.
Peace,
Matt.
From: Xinyang Liu <xinyang_ie...@163.com>
Date: Wednesday, April 4, 2018 at 2:36 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear Matthew,
Thank you very much for your kind reply!
Could I continue asking two more new questions?
1. In the preprocessed structural data, both the
/${Subject}/T1w/fsaverage_LR32k and /${Subject}/MNINonLinear/fsaverage_LR32k
contain white surface files with the same names, such as
"${Subject}.L.white.32k_fs_LR.surf.gii" and
"${Subject}.L.white.MSMAll.32k_fs_LR.surf.gii". Is there any difference
between these files of the same name but under different routes?
2. I am kind of confusing about the space transformation in surface ROI fibre
tracking. In the volume-based analysis, there is native diffusion space and
standard space, and tractograhpy is done in native diffusion space. For surface
data, I suppose the files like "${Subject}.L.white.32k_fs_LR.surf.gii" have
already been registered to a 32k standard mesh. Then should the surface ROI
fibre tracking go back to native space and how if needed?
Best regards,
Xinyang
At 2018-04-04 00:49:09, "Glasser, Matthew" <glass...@wustl.edu> wrote:
1. Yes, though they can come from a certain (configurable) radius around the
vertex, rather than all from the point location with --sampvox.
2. I think probtrackx2 looks for greater than zero, but you could of course
binarize them.
3. I believe you can display the surface counts in GIFTI format with --fopd,
you might ask more on the FSL list as I haven’t done much tractorgraphy in a
while.
Peace,
Matt.
From: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu
<xinyang_ie...@163.com>
Date: Tuesday, April 3, 2018 at 1:52 AM
To: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear HCP experts,
Hi. As a new learner of the HCP tfMRI surface data, I have some questions when
using them as ROIs to do probabilistic tractography. I would be very thankful
to receive any of your kind guidance. My questions are as below.
1. I know that in FSL probtrackx2 voxel-based fibre tracking, 5000 streamlines
(default) come out from each voxel. How about the case in the surface vertices
of the HCP grayordinate space? Is it similar with the voxel-based tracking,
like 5000 streamlines coming out from each vertex?
2.The tfMRI surface ROIs usually contain information of signal intensities,
would this influence the diffusion tracking results if using them as masks?
3. How to display the surface ROIs (.func.gii or .asc) and output tracking
paths (.nii.gz in FSL results) in the same figure?
Look forward to your feedbacks. Thank you very much！
Best regards,
Xinyang Liu
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
