: Friday, February 27, 2015 10:45 AM
To: Archer,Derek B
Cc: hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
Hi Derek
With the default burn-in period (b=1000 iterations), on a CPU cluster you
should expect ~10 hours per subject
,Derek B
*Cc:* hcp-users@humanconnectome.org
*Subject:* Re: [HCP-Users] Processing Diffusion MRI Data
Hi Derek
With the default burn-in period (b=1000 iterations), on a CPU cluster
you should expect ~10 hours per subject. We are using a GPU cluster, so it
takes us much less than that.
It’s
Sent: Friday, February 27, 2015 10:45 AM
To: Archer,Derek B
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
Hi Derek
With the default burn-in period (b=1000 iterations), on a CPU cluster you
should expect ~10 hours per subject. We are using a GPU cluster, so
Hi Stam,
Thank you for the fast response!
Derek
From: Stamatios Sotiropoulos [mailto:stamatios.sotiropou...@ndcn.ox.ac.uk]
Sent: Friday, February 27, 2015 10:46 AM
To: Archer,Derek B
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
Hi Derek
, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Tuesday, February 17, 2015 12:55 PM
To: Archer,Derek B; Stamatios Sotiropoulos;
hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
Are you running the command on ${StudyFolder
: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Tuesday, February 17, 2015 12:55 PM
To: Archer,Derek B; Stamatios Sotiropoulos; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
Are you running the command on ${StudyFolder}/${Subject}/T1w/Diffusion
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
Why do you need to use FLIRT/FNIRT with already registered data? As for the
others and aside from the flags you already mention, I think the recommendation
for bedpostX will include these flags:
-n 3 (for 3 fibers)
--cnonlinear
--rician
--model=3
@humanconnectome.org
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
Why do you need to use FLIRT/FNIRT with already registered data? As for the
others and aside from the flags you already mention, I think the recommendation
for bedpostX will include these flags:
-n 3 (for 3 fibers)
--cnonlinear
--rician
*Subject:* Re: [HCP-Users] Processing Diffusion MRI Data
Hi Derek
Please notice that model=3 is not officially released yet in FSL. Also,
there should be a future HCP release in the near future including bedpostx
results, with the optimal parameters.
Stam
On 16 Feb 2015, at 16:25
, Stamatios Sotiropoulos stamatios.sotiropou...@ndcn.ox.ac.uk, hcp-users@humanconnectome.org
hcp-users@humanconnectome.org
Subject: RE: [HCP-Users] Processing Diffusion MRI Data
Hi Matt,
The exact command I’m using locally is (I tried this from Stam’s input):
bedpostx subject directory –n 3
@humanconnectome.orgmailto:hcp-users@humanconnectome.org
Subject: [HCP-Users] Processing Diffusion MRI Data
Hello,
I am trying to analyze the preprocessed diffusion data, however, I am having
some difficulties. Is there some documentation that I could look at that
outlines how to use bedpostx, FLIRT
Hello,
I am trying to analyze the preprocessed diffusion data, however, I am having
some difficulties. Is there some documentation that I could look at that
outlines how to use bedpostx, FLIRT/FNIRT, DTIFIT and probtrackx with this data?
From what I've found in the archives, I need to do the
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