Re: [HCP-Users] Resting State processing

[Glasser, Matthew]

Does the file exist?  That might be the old config file it is looking for 
suggesting that you don’t have the latest master.

Peace,

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, January 8, 2018 at 9:15 AM
To: "hcp-users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] Resting State processing

Hello all,

Despite having the most recent version of the hcp pipeline (3.22) and 
downloading the MSM configuration binaries, however, I am still receiving an 
error when I attempt to run the PreFreeSurfer pipeline with RegName="MSMSulc". 
This is the error message I receive: 
/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
 Couldn't open the file!

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

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Re: [HCP-Users] connectivity matrices

[Glasser, Matthew]

That might be better answered on the FSL list.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Monday, January 8, 2018 at 8:23 AM
To: HCP 讨论组 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] connectivity matrices

Dear HCP experts,

Hi. We are doing brain structural network study based on HCP diffusion data and 
FSL. We want to acquire 90*90 and 1024*1024 ROI connectivity matrices of the 
whole brain, which is based on probabilistic tracing with the FSL probtrackx2 
--network mode. However, our running always got killed probably due to the 
limitation memory of the CPU. Could you please suggest a way for us to finish 
the running? For example, do we need split the matrix with some commands like 
-rseed in probtrackx2? Or is there any other approaches? Any guidance would be 
very appreciated. Thanks!

Best regards,
Xinyang Liu







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Re: [HCP-Users] A question about the geodesic distance

[Timothy Coalson]

To clarify further, until a surface registration is done, there is no
obvious relationship between the vertices of one subject and another (and
the surfaces even have different numbers of vertices).  After registration
and resampling to a standard mesh (MSMAll and fs_LR 32k are options for
these operations), the surfaces have the same number of vertices across
subjects, and additionally the same vertex index has close to the same
neuroanatomical meaning in each subject (how close it is is determined by
what registration was used).

Tim


On Sun, Jan 7, 2018 at 11:59 AM, Glasser, Matthew 
wrote:

> If by brain vertex you mean neuroanatomically corresponding points, then
> yes, this would be a sensible thing to do after MSMAll registration.
>
> Peace,
>
> Matt.
>
> From: Aaron C 
> Date: Sunday, January 7, 2018 at 11:56 AM
> To: Matt Glasser , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
>
> Subject: Re: [HCP-Users] A question about the geodesic distance
>
> Hi Matt,
>
>
> Thank you for looking into my question. I am trying to compare geodesic
> distance between a given pair of brain vertices across different subjects,
> so I hope I would be able to locate the same brain vertex in different
> subjects. Is this feasible using the data after MSM-All registration?
> Thank you.
>
>
> Aaron
>
> *From:* Glasser, Matthew 
> *Sent:* Wednesday, January 3, 2018 10:41 PM
> *To:* Aaron C; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] A question about the geodesic distance
>
> This question appears to presume a standard mesh meaning some kind of
> registration has occurred.  I think you need to be a bit more specific
> about what you are wanting to do.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Aaron C <
> aaroncr...@outlook.com>
> Date: Wednesday, January 3, 2018 at 8:19 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] A question about the geodesic distance
>
> Dear HCP experts,
>
>
> I have a question about the geodesic distance with respect to the MSM-All
> registration. Given a pair of brain vertices, is the variance of their
> geodesic distance across different subjects still preserved after MSM-All
> registration? Thank you.
>
> ___
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Re: [HCP-Users] A question about the geodesic distance

[Aaron C]

Hi Matt,


Thank you for looking into my question. I am trying to compare geodesic 
distance between a given pair of brain vertices across different subjects, so I 
hope I would be able to locate the same brain vertex in different subjects. Is 
this feasible using the data after MSM-All registration? Thank you.


Aaron

From: Glasser, Matthew 
Sent: Wednesday, January 3, 2018 10:41 PM
To: Aaron C; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A question about the geodesic distance

This question appears to presume a standard mesh meaning some kind of 
registration has occurred.  I think you need to be a bit more specific about 
what you are wanting to do.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Wednesday, January 3, 2018 at 8:19 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] A question about the geodesic distance


Dear HCP experts,


I have a question about the geodesic distance with respect to the MSM-All 
registration. Given a pair of brain vertices, is the variance of their geodesic 
distance across different subjects still preserved after MSM-All registration? 
Thank you.

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Re: [HCP-Users] Resting State processing

[Timothy Hendrickson]

Hello all,

Despite having the most recent version of the hcp pipeline (3.22) and
downloading the MSM configuration binaries, however, I am still receiving
an error when I attempt to run the PreFreeSurfer pipeline with
RegName="MSMSulc". This is the error message I receive:
*/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
Couldn't open the file!*
-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

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[HCP-Users] connectivity matrices

[Xinyang Liu]

Dear HCP experts,


Hi. We are doing brain structural network study based on HCP diffusion data and 
FSL. We want to acquire 90*90 and 1024*1024 ROI connectivity matrices of the 
whole brain, which is based on probabilistic tracing with the FSL probtrackx2 
--network mode. However, our running always got killed probably due to the 
limitation memory of the CPU. Could you please suggest a way for us to finish 
the running? For example, do we need split the matrix with some commands like 
-rseed in probtrackx2? Or is there any other approaches? Any guidance would be 
very appreciated. Thanks!


Best regards,
Xinyang Liu





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