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" 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: on behalf of Xinyang Liu
Date: Tuesday, April 3, 2018 at 1:52 AM
To: HCP 讨论组
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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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
___
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Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
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 mailto:xinyang_ie...@163.com>>
Date: Wednesday, April 4, 2018 at 2:36 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP 讨论组
mailto: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"
mailto: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:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Tuesday, April 3, 2018 at 1:52 AM
To: HCP 讨论组
mailto: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
Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
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, we used
"$SUBJECT/MNINonLinear/fsaverage_LR32k/$SUBJECT.L.midthickness._MSMAll.32k_fs_LR.surf.gii"
to do the multiplication. Then I suppose the surface ROI to be acquired in the
MNI standard space, and therefore need to use the --xfm and --invxfm in
probtrackx2. Is my understanding correct?
2. In this way, do the HCP data contain files that can be used in --xfm,
--invxfm and --seedref in surface prob-tracking?
3. In the FSL "surf2surf" format conversion from .func.gii to ASCII type
(.asc), is it correct to use
"$Subject/MNINonLinear/fsaverage_LR32k/${Subject}.R.white.32k_fs_LR.surf.gii"
as the input (-i) and the acquired "ROI.func.gii" as --value?
Look forward to your kind guidance. Thanks a lot!
Best regards,
Xinyang
At 2018-04-04 18:44:25, "Glasser, Matthew" 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
Date: Wednesday, April 4, 2018 at 2:36 AM
To: Matt Glasser
Cc: HCP 讨论组
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" 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: on behalf of Xinyang Liu
Date: Tuesday, April 3, 2018 at 1:52 AM
To: HCP 讨论组
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] -surface-distortion -local-affine-method
Hi, I am trying to run the PostFreeSurfer step using the latest Pipelines-master (downloaded today 04 April 2018 from github) but I get an error while running the script FreeSurfer2CaretConvertAndRegisterNonlinear.sh: ERROR: Unexpected parameter: -local-affine-method It seems the wb_command -surface-distortion does not have the option for "-local-affine-method" although I have the latest version of workbench (v1.2.3). The source code seems to have this option though here: https://github.com/Washington-University/workbench/commit/576dbfba0f66b7cf5c0b1b58e660c3ffe8e6b356 Do I have to update my local workbench version to incorporate the source code updates? Thanks Moataz ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] -surface-distortion -local-affine-method
That feature isn’t yet in the released wb_command. Try using the latest “released” version of the Pipelines from GitHub, rather than the master branch. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of Moataz Assem Date: Wednesday, April 4, 2018 at 1:30 PM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] -surface-distortion -local-affine-method Hi, I am trying to run the PostFreeSurfer step using the latest Pipelines-master (downloaded today 04 April 2018 from github) but I get an error while running the script FreeSurfer2CaretConvertAndRegisterNonlinear.sh: ERROR: Unexpected parameter: -local-affine-method It seems the wb_command –surface-distortion does not have the option for “–local-affine-method” although I have the latest version of workbench (v1.2.3). The source code seems to have this option though here: https://github.com/Washington-University/workbench/commit/576dbfba0f66b7cf5c0b1b58e660c3ffe8e6b356 Do I have to update my local workbench version to incorporate the source code updates? Thanks Moataz ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Inline replies to some comments.
Tim
On Wed, Apr 4, 2018 at 7:38 AM, Xinyang Liu 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" 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
> Date: Wednesday, April 4, 2018 at 2:36 AM
> To: Matt Glasser
> Cc: HCP 讨论组
> 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" 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: on behalf of Xinyang Liu <
> xinyang_ie...@163.com>
> Date: Tuesday, April 3, 2018 at 1:52 AM
> To: HCP 讨论组
> 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 (de
