Re: [HCP-Users] BedpostX for 7T Diffusion data

[Elam, Jennifer]

Hi Kamal,

No, we have not released bedpostX processed 7T diffusion data on HCP Young 
Adult subjects due to competing priorities, such as the advent of the Lifespan 
HCP-Development and HCP-Aging projects.


Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Shadi, Kamal 

Sent: Thursday, April 25, 2019 6:49:11 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] BedpostX for 7T Diffusion data


Dear HCP experts,



Is bedpostx data available for 7T dMRI scans?



Regards,

Kamal

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Re: [HCP-Users] "activation" tables for reporting pscalar results

[David Van Essen]

Spherical coordinates (latitude and longitude) concisely encode precise 
locations on an atlas surface and on individuals registered to the atlas in a 
way that respects cortical surface topology. Thus, they have inherent 
advantages over conventional stereotaxic coordinates in the context of the 
current thread.

Spherical coordinates were proposed years ago by my lab 
(https://www.pnas.org/content/95/3/788; 
https://www.sciencedirect.com/science/article/pii/S0042698901000451) and by 
Fischl et al. 
(https://www.sciencedirect.com/science/article/pii/S1053811998903962). 
Reporting locations using latitude and longitude has yet to become routine 
practice in neuroimaging - but it’s not too late to start!

David

> On Apr 25, 2019, at 9:33 AM, Joseph Orr  wrote:
> 
> Thanks for all the input on this, its been helpful.
> --
> Joseph M. Orr, Ph.D.
> Assistant Professor
> Department of Psychological and Brain Sciences
> Texas A Institute for Neuroscience
> Texas A University
> College Station, TX
> 
> 
> On Wed, Apr 24, 2019 at 7:34 PM Glasser, Matthew  > wrote:
> I do not report MNI coordinates for any studies because I don’t think they 
> add a lot of value for the reasons described in Tim’s PNAS paper.  Studies 
> that provide actual results on the surface are much more useful, and I have 
> extensively used such studies to make incisive neuroanatomical comparisons.  
> I’ve also yet to be asked to provide MNI coordinates by a peer reviewer.  I 
> think if you share the actual data, MNI coordinates are superfluous and if 
> you use a well defined neuroanatomical parcellation such as the HCP’s 
> multi-modal parcellation, it is fine to talk about findings in particular 
> brain areas (if you actually check to see that your findings overlap with the 
> brain areas you name—i.e. don’t just eyeball vs a picture on the wall).  
> 
> Matt.
> 
> From:  > on behalf of Timothy Coalson 
> mailto:tsc...@mst.edu>>
> Date: Wednesday, April 24, 2019 at 1:47 PM
> To: Joseph Orr mailto:joseph@tamu.edu>>
> Cc: HCP Users  >
> Subject: Re: [HCP-Users] "activation" tables for reporting pscalar results
> 
> We recommend sharing the results as data files (as mentioned, this is the 
> intent of BALSA), even if you choose to report MNI coordinates in the text.  
> Something to keep in mind is that group average surfaces do not behave like 
> group average volume data, the surface gets smoothed out wherever folding 
> patterns aren't fully aligned, resulting in a surface that does not approach 
> gyral crowns or sulcal fundi (most notably with functional alignment such as 
> MSMAll - freesurfer-aligned surfaces will average to something with more 
> folding preserved, at the cost of functional locality, but there are still 
> locations with high variability in folding patterns across subjects that will 
> still get smoothed out on a group average surface).  See supplementary 
> material, figure S1, and figure S9 panel B2, from our paper on the effects of 
> volume-based methods:
> 
> https://www.ncbi.nlm.nih.gov/pubmed/29925602 
> 
> 
> If meta analysis of this sort is only intended to give a very rough idea of 
> location, even this may not be a deal breaker.  You can use wb_command 
> -surface-coordinates-to-metric to get the coordinates as data, use 
> -cifti-create-dense-from-template to convert that to cifti, and then use 
> -cifti-parcellate on that to get center of gravity coordinates of the 
> vertices used.  Note that these center of gravity coordinates could be a 
> distance away from the surface, due to curvature.
> 
> Tim
> 
> 
> On Wed, Apr 24, 2019 at 11:06 AM Joseph Orr  > wrote:
> True - these kind of tools generally assume certain degrees of smoothing, 
> which isn't the case with surface-based. And activation based meta-analysis 
> will apply a kernel that will likely extend outside the brain for a surface 
> activation that is not within a sulcus. I'd be curious to hear what those 
> more familiar with meta-analytic methods think about how surface-based 
> results can be incorporated with volumetric results. 
> --
> Joseph M. Orr, Ph.D.
> Assistant Professor
> Department of Psychological and Brain Sciences
> Texas A Institute for Neuroscience
> Texas A University
> College Station, TX
> 
> 
> On Wed, Apr 24, 2019 at 11:00 AM Harms, Michael  > wrote:
>  
> 
> Well, that raises the question if surface-based results should just be 
> automatically “lumped in” with volume-based results by tools such as 
> neurosynth to begin with…
> 
>  
> 
> -- 
> 
> Michael Harms, Ph.D.
> 
> 

Re: [HCP-Users] Probabilistic tractography for dense connectome

[Stamatios Sotiropoulos]

Hi Aaron

You need the PreTractography script, available in one of the branches of the 
WU-pipelines.

https://github.com/Washington-University/HCPpipelines/tree/diffusion-tractography/DiffusionTractography

Best wishes
Stam



On 26 Apr 2019, at 15:50, Aaron C 
mailto:aaroncr...@outlook.com>> wrote:

Hi Matt,

Thank you for letting me know. The full command I mentioned is as follows:

probtrackx2 --samples=../T1w/Diffusion.bedpostX/merged \
--mask=../T1w/Diffusion.bedpostX/nodif_brain_mask \
--xfm=xfms/standard2acpc_dc \
--invxfm=xfms/acpc_dc2standard --seedref=T1w_restore.2.nii.gz \
--loopcheck --forcedir -c 0.2 --sampvox=2 --randfib=1 \
--stop=Connectome/stop --wtstop=Connectome/wtstop \
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \
-x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \
--target3=Connectomes/GrayOrdinates.txt --dir=Connectomes

It's in the HCP course practical "Fibre Orientation Models and Tractography 
Analysis" taught by Matteo Bastiani. Thank you.

From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Thursday, April 25, 2019 7:04 PM
To: Aaron C; hcp-users@humanconnectome.org
Cc: Stamatios Sotiropoulos
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

Not as far as I am aware, but Stam might know.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Thursday, April 25, 2019 at 9:15 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Probabilistic tractography for dense connectome

Dear HCP experts,

I have a question about the probabilistic tractography command used for 
generating dense connectome 
(https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7). Are there any 
shared scripts for generating "pial.L.asc", "white.L.asc", 
"Whole_Brain_Trajectory_ROI_2.nii.gz", and the files such as 
"CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz" used in the probabilistic tractography 
command?
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Re: [HCP-Users] Probabilistic tractography for dense connectome

[Aaron C]

Hi Matt,

Thank you for letting me know. The full command I mentioned is as follows:

probtrackx2 --samples=../T1w/Diffusion.bedpostX/merged \
--mask=../T1w/Diffusion.bedpostX/nodif_brain_mask \
--xfm=xfms/standard2acpc_dc \
--invxfm=xfms/acpc_dc2standard --seedref=T1w_restore.2.nii.gz \
--loopcheck --forcedir -c 0.2 --sampvox=2 --randfib=1 \
--stop=Connectome/stop --wtstop=Connectome/wtstop \
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \
-x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \
--target3=Connectomes/GrayOrdinates.txt --dir=Connectomes

It's in the HCP course practical "Fibre Orientation Models and Tractography 
Analysis" taught by Matteo Bastiani. Thank you.

From: Glasser, Matthew 
Sent: Thursday, April 25, 2019 7:04 PM
To: Aaron C; hcp-users@humanconnectome.org
Cc: Stamatios Sotiropoulos
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

Not as far as I am aware, but Stam might know.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Thursday, April 25, 2019 at 9:15 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Probabilistic tractography for dense connectome

Dear HCP experts,

I have a question about the probabilistic tractography command used for 
generating dense connectome 
(https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7). Are there any 
shared scripts for generating "pial.L.asc", "white.L.asc", 
"Whole_Brain_Trajectory_ROI_2.nii.gz", and the files such as 
"CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz" used in the probabilistic tractography 
command?

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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.

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