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 
 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 
as the input (-i) and the acquired "ROI.func.gii" as --value? 

Look forward to your kind guidance. Thanks a lot!

Best regards,

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.



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 
"${Subject}" and 
"${Subject}".  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}" 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,

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 



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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