files to use for the analysis

[Xiuyi Wang]

Hello experts,

I would like to investigate the lateralization effect of the myelin map, cortical thickness map, surface area, and the geodesic distance matrix using Glasser's parcellation.

Do I need to use the following maps?

1). Myelin map

../${subj_ID}/MNINonLinear/fsaverage_LR32k/${subj_ID}.MyelinMap_MSMAll.32k_fs_LR.dscalar.nii

2). Cortical thickness map 

../${subj_ID}/MNINonLinear/fsaverage_LR32k/${subj_ID}.thickness_MSMAll.32k_fs_LR.dscalar.nii

3). The surf file to calculate the surface area and geodesic distance matrix

../${subj_ID}/MNINonLinear/fsaverage_LR32k/${subj_ID}.${hemi}.midthickness_MSMAll.32k_fs_LR.surf.gii

Many thanks for your confirmation.

Xiuyi

[Glasser, Matthew]

1. Yes, though we will have a preprint out soon (hopefully in a couple of weeks) that would have a major impact on the interpretation of any such analysis.  It deals with correction of residual B1+ transmit field effects in the T1w/T2w myelin maps.  These effects are lateralized (and in fact it is this very property that allows us to get initial purchase on them for correction).   
2. This is the real cortical thickness. If you wanted the thickness compensated for folding effects (e.g. if you were considering cortical thickness as a property of cortical areas regardless of where on a fold they are), you could use corrthickness.
3. Yes.  There are also _va .shape.gii files that have surface area computed for each vertex.

 

Matt.

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[Xiuyi Wang]

Hello Matt,

Many thanks for your confirmation. 

1), Do you mean your recent study suggests that the lateralization effect of myeline maps may be driven by the residual B1+ transmit field effects in the T1w/T2w myelin maps, rather than the real lateralization effect?

2), That's very helpful. Many thanks.

3), That's great. But I did not find any files containing the '_va.shape.gii' in the MNINonLinear/fsaverage_LR32k folder. Could you please provide me with more info about the location of this file?

    The files I found are:

Many thanks.

Xiuyi

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[Glasser, Matthew]

1) Basically yes.  The residual looks mostly like L/R folding misalignments of cortical areas.

3) Look in T1w/fsaverage_LR32k.

 

Matt.

 

From: 'Xiuyi Wang' via HCP-Users <hcp-...@humanconnectome.org>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, April 22, 2021 at 5:39 AM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] files to use for the analysis

 

 

Hello Matt,

 

Many thanks for your confirmation. 

 

1), Do you mean your recent study suggests that the lateralization effect of myeline maps may be driven by the residual B1+ transmit field effects in the T1w/T2w myelin maps, rather than the real lateralization effect?

 

2), That's very helpful. Many thanks.

 

3), That's great. But I did not find any files containing the '_va.shape.gii' in the MNINonLinear/fsaverage_LR32k folder. Could you please provide me with more info about the location of this file?

 

    The files I found are:

 

Many thanks.

 

Xiuyi

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[Xiuyi Wang]

Hello Matt,

Thanks.

1). That's good to know. Does the residual B1+ transmit field effects in the T1w/T2w myelin maps also influence the lateralization effect of cortical thickness, surface area, and geodesic distance?

3). Thanks. I found it. 

Xiuyi

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[Glasser, Matthew]

1. It’s possible but will depend on how good of a jobs the surface reconstruction is.

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[Xiuyi Wang]

Okay, thanks. I will think about it. 

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/163154F4-2DF3-4E2A-949D-6DB84C8794C3%40wustl.edu.

[Coalson, Timothy Scott (S&T-Student)]

If you want your measurements to reflect the original shape of the subject's brain, you should use files from T1w/ whenever possible.  Anything that contains coordinates in the MNINonLinear folder has gone through FNIRT registration to the MNI template, and no longer reflects the subject's original head size, etc.

However, we do not recompute things like thickness after transforming to MNINonLinear space, so there are some files in MNINonLinear/ that reflect the original anatomy in some way.

Tim

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From: 'Xiuyi Wang' via HCP-Users <hcp-...@humanconnectome.org>

Sent: Thursday, April 22, 2021 5:39 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] files to use for the analysis

 

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CAF163upiyozhOzxY6ZLjHz5k13wiERvhYqFF5ni3g7VwmghYrA%40mail.gmail.com.