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
>
>
>
>
>
>
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