Re: [HCP-Users] software to do deterministic tractography

2018-02-01 Thread Xinyang Liu 
Dear Matt,


That's really a great idea! I will try it then. Thanks a lot.
By the way, for HCP data probabilistic tractography, are there suggested values 
for basic parameters like --nsamples, --nsteps, and --steplength ? For example, 
the dMRI resolution is 1.25mm, and the default --steplength is 0.5 mm. Does it 
matter if that is not a integral multiple relationship ?


Best regards,
Xinyang



At 2018-02-01 19:47:59, "Glasser, Matthew" <glass...@wustl.edu> wrote:

You can run with fewer --nsamples multiple runs of probtrackx2 on different 
computers each with a different --rseed and then combine them afterwards for a 
full dataset.


Peace,


Matt.


From: Xinyang Liu <xinyang_ie...@163.com>
Date: Thursday, February 1, 2018 at 5:44 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] software to do deterministic tractography



Dear Matt,


Sorry I didn't get the point. Could you please explain more in detail?  Your 
suggestion would be very important and helpful to us. Thank you very much.


Best regards,
Xinyang



At 2018-02-01 19:30:12, "Glasser, Matthew" <glass...@wustl.edu> wrote:

You can parallelize with fewer samples and using different random numbers and 
then combine after the fact.


Peace,


Matt.


From: Xinyang Liu <xinyang_ie...@163.com>
Date: Thursday, February 1, 2018 at 5:20 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] software to do deterministic tractography



Dear Matt,


Thanks a lot for your suggestion. Actually, probabilistic tractography with FSL 
was our first choice with HCP data. However, the executing time was too long 
when we tried to build a global network for single subject with FSL 
probtrackx2, and we don't know how to run in parallel without GPU. Therefore, 
we wanna try the deterministic way to shorten the time. 


Best,
Xinyang



At 2018-02-01 18:51:47, "Glasser, Matthew" <glass...@wustl.edu> wrote:

In general we recommend probabilistic tractography with FSL, but other options 
include MRTriX.


Peace,


Matt.


From: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu 
<xinyang_ie...@163.com>
Date: Thursday, February 1, 2018 at 3:14 AM
To: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: [HCP-Users] software to do deterministic tractography



Dear HCP experts,


Could you please recommend us some software for the deterministic tractography 
analysis of HCP data? We are at the beginning to do that and wondering what to 
choose for the high-quality data. Any suggestions would be very appreciated. 
Thanks.


Best regards,
Xinyang Liu





 

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Re: [HCP-Users] software to do deterministic tractography

2018-02-01 Thread Glasser, Matthew 
You can run with fewer --nsamples multiple runs of probtrackx2 on different 
computers each with a different --rseed and then combine them afterwards for a 
full dataset.

Peace,

Matt.

From: Xinyang Liu <xinyang_ie...@163.com<mailto:xinyang_ie...@163.com>>
Date: Thursday, February 1, 2018 at 5:44 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: HCP 讨论组 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] software to do deterministic tractography

Dear Matt,

Sorry I didn't get the point. Could you please explain more in detail?  Your 
suggestion would be very important and helpful to us. Thank you very much.

Best regards,
Xinyang


At 2018-02-01 19:30:12, "Glasser, Matthew" 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
You can parallelize with fewer samples and using different random numbers and 
then combine after the fact.

Peace,

Matt.

From: Xinyang Liu <xinyang_ie...@163.com<mailto:xinyang_ie...@163.com>>
Date: Thursday, February 1, 2018 at 5:20 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: HCP 讨论组 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] software to do deterministic tractography

Dear Matt,

Thanks a lot for your suggestion. Actually, probabilistic tractography with FSL 
was our first choice with HCP data. However, the executing time was too long 
when we tried to build a global network for single subject with FSL 
probtrackx2, and we don't know how to run in parallel without GPU. Therefore, 
we wanna try the deterministic way to shorten the time.

Best,
Xinyang


At 2018-02-01 18:51:47, "Glasser, Matthew" 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
In general we recommend probabilistic tractography with FSL, but other options 
include MRTriX.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu <xinyang_ie...@163.com<mailto:xinyang_ie...@163.com>>
Date: Thursday, February 1, 2018 at 3:14 AM
To: HCP 讨论组 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] software to do deterministic tractography

Dear HCP experts,

Could you please recommend us some software for the deterministic tractography 
analysis of HCP data? We are at the beginning to do that and wondering what to 
choose for the high-quality data. Any suggestions would be very appreciated. 
Thanks.

Best regards,
Xinyang Liu





___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users









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HCP-Users@humanconnectome.org
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Re: [HCP-Users] software to do deterministic tractography

2018-02-01 Thread Xinyang Liu 
Dear Matt,


Sorry I didn't get the point. Could you please explain more in detail?  Your 
suggestion would be very important and helpful to us. Thank you very much.


Best regards,
Xinyang



At 2018-02-01 19:30:12, "Glasser, Matthew" <glass...@wustl.edu> wrote:

You can parallelize with fewer samples and using different random numbers and 
then combine after the fact.


Peace,


Matt.


From: Xinyang Liu <xinyang_ie...@163.com>
Date: Thursday, February 1, 2018 at 5:20 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] software to do deterministic tractography



Dear Matt,


Thanks a lot for your suggestion. Actually, probabilistic tractography with FSL 
was our first choice with HCP data. However, the executing time was too long 
when we tried to build a global network for single subject with FSL 
probtrackx2, and we don't know how to run in parallel without GPU. Therefore, 
we wanna try the deterministic way to shorten the time. 


Best,
Xinyang



At 2018-02-01 18:51:47, "Glasser, Matthew" <glass...@wustl.edu> wrote:

In general we recommend probabilistic tractography with FSL, but other options 
include MRTriX.


Peace,


Matt.


From: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu 
<xinyang_ie...@163.com>
Date: Thursday, February 1, 2018 at 3:14 AM
To: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: [HCP-Users] software to do deterministic tractography



Dear HCP experts,


Could you please recommend us some software for the deterministic tractography 
analysis of HCP data? We are at the beginning to do that and wondering what to 
choose for the high-quality data. Any suggestions would be very appreciated. 
Thanks.


Best regards,
Xinyang Liu





 

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





 
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] software to do deterministic tractography

2018-02-01 Thread Xinyang Liu 
Dear Matt,


Thanks a lot for your suggestion. Actually, probabilistic tractography with FSL 
was our first choice with HCP data. However, the executing time was too long 
when we tried to build a global network for single subject with FSL 
probtrackx2, and we don't know how to run in parallel without GPU. Therefore, 
we wanna try the deterministic way to shorten the time. 


Best,
Xinyang



At 2018-02-01 18:51:47, "Glasser, Matthew"  wrote:

In general we recommend probabilistic tractography with FSL, but other options 
include MRTriX.


Peace,


Matt.


From:  on behalf of Xinyang Liu 

Date: Thursday, February 1, 2018 at 3:14 AM
To: HCP 讨论组 
Subject: [HCP-Users] software to do deterministic tractography



Dear HCP experts,


Could you please recommend us some software for the deterministic tractography 
analysis of HCP data? We are at the beginning to do that and wondering what to 
choose for the high-quality data. Any suggestions would be very appreciated. 
Thanks.


Best regards,
Xinyang Liu





 

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HCP-Users@humanconnectome.org
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