Re: [HCP-Users] Some questions about data quality check

[Glasser, Matthew]

1.  FreeSurfer does not fully segment the hippocampus on the surface.
2.  I probably wouldn’t look at this in this way.  In general, one wants the 
brain to be roughly aligned well without major obvious deformations.  If you 
want an example of too much distortion, try ANTs.
3.  The parcellation is available here https://balsa.wustl.edu/file/show/3VLx 
and you can use wb_command -cifti-parcellate across rows and columns of a dense 
connectome that has been tracked to the surface.  As far as generating such a 
dense connectome with FSL, I think there might be some scripts floating around 
in the GitHub.  I would have a look at the diffusion lectures and see what they 
suggest.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Wednesday, February 13, 2019 at 12:27 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Some questions about data quality check

Dear HCP experts,

I have some questions about data quality check when using the HCP pipeline.

1. In the panel on the lower left corner on page 23 of the data quality slides 
(https://wustl.app.box.com/s/krekn5svmg4rgig2ossqqhuhcbrgg8c6), is the brain 
segmentation there missing some parts of the temporal lobe?

2. On page 25 of the slides, what's the criteria of determine "good" or "bad" 
volume distortion? Fewer number of above-threshold blobs the better?

I also have a question about structural connectome of the HCP diffusion data. 
Is there any shared script to generate parcel to parcel structural connectivity 
using Dr. Glasser's multi-modal parcellation scheme? Thank you.

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Re: [HCP-Users] Some questions about data quality check

[Harms, Michael]

Another way to put this is that hippocampus is not cortical (it is part of the 
medial wall), and thus FreeSurfer does not attempt to generate surfaces that 
follow the structures in that region.  They even have a FAQ on that specific 
question:

https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfacesnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingthestructuresthere.HowcanIfixthis.3F

cheers,
-MH

--
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 "Reid, Erin" 

Date: Wednesday, February 13, 2019 at 11:13 AM
To: Aaron C 
Cc: "hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] Some questions about data quality check

Hello Aaron,

1. The hippocampus is a known area that FreeSurfer has a little difficulty with 
so we don’t expect perfection in that area.  The subject shown in the document 
is quite good however.

2. Yes, "good" volume distortion has fewer blobs.  The blobs are indicating 
where the individual surface was manipulated in order to register to the atlas. 
 So the fewer manipulations the better.

Hope this helps.

Erin


On Feb 13, 2019, at 12:27 AM, Aaron C 
mailto:aaroncr...@outlook.com>> wrote:

Dear HCP experts,

I have some questions about data quality check when using the HCP pipeline.

1. In the panel on the lower left corner on page 23 of the data quality slides 
(https://wustl.app.box.com/s/krekn5svmg4rgig2ossqqhuhcbrgg8c6), is the brain 
segmentation there missing some parts of the temporal lobe?

2. On page 25 of the slides, what's the criteria of determine "good" or "bad" 
volume distortion? Fewer number of above-threshold blobs the better?

I also have a question about structural connectome of the HCP diffusion data. 
Is there any shared script to generate parcel to parcel structural connectivity 
using Dr. Glasser's multi-modal parcellation scheme? Thank you.
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The materials in this message are private and may contain Protected Healthcare 
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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.

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Re: [HCP-Users] Some questions about data quality check

[Reid, Erin]

Hello Aaron,

1. The hippocampus is a known area that FreeSurfer has a little difficulty with 
so we don’t expect perfection in that area.  The subject shown in the document 
is quite good however.

2. Yes, "good" volume distortion has fewer blobs.  The blobs are indicating 
where the individual surface was manipulated in order to register to the atlas. 
 So the fewer manipulations the better.

Hope this helps.

Erin

On Feb 13, 2019, at 12:27 AM, Aaron C 
mailto:aaroncr...@outlook.com>> wrote:

Dear HCP experts,

I have some questions about data quality check when using the HCP pipeline.

1. In the panel on the lower left corner on page 23 of the data quality slides 
(https://wustl.app.box.com/s/krekn5svmg4rgig2ossqqhuhcbrgg8c6), is the brain 
segmentation there missing some parts of the temporal lobe?

2. On page 25 of the slides, what's the criteria of determine "good" or "bad" 
volume distortion? Fewer number of above-threshold blobs the better?

I also have a question about structural connectome of the HCP diffusion data. 
Is there any shared script to generate parcel to parcel structural connectivity 
using Dr. Glasser's multi-modal parcellation scheme? Thank you.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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