Hi Matt,
The exact command I'm using locally is (I tried this from Stam's input):
bedpostx <subject directory> -n 3 -model 2 -g -rician
Subject directory contents:
bvals
bvecs
data.nii.gz
nodif_brain_mask.nii.gz
grad_dev.nii.gz
This works. How long do you estimate this will take? Because the -g option is
not available on the cluster I am working on (not sure why this is the case..),
and I think that may be causing the issue.
Thanks,
Derek
From: Glasser, Matthew [mailto:[email protected]]
Sent: Tuesday, February 17, 2015 12:47 PM
To: Archer,Derek B; Stamatios Sotiropoulos; [email protected]
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
How about posting the exact command line you are using and a listing of the
contents of <subject_directory>
Peace,
Matt.
From: <Archer>, Derek B <[email protected]<mailto:[email protected]>>
Date: Tuesday, February 17, 2015 at 9:20 AM
To: Stamatios Sotiropoulos
<[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] Processing Diffusion MRI Data
Hi Matt and Stam,
I seem to still be having some sort of issue running bedpostx. I'm using:
bedpostx <subject_directory> --cnonlinear --rician --model=2 --nf=3.
(The -g option is not available in my version of FSL (5.0.5). I am on a
cluster environment.)
So when I run this line of code, I get the following error:
** ERROR: nifti_convert_nhdr2nim: bad dim[0]
** ERROR: (nifti_image_read): cannot create nifty image from header 'data'
** ERROR: nifti_image_open (data): bad header info
** ERROR: failed to open file data
The error seems to be with data.nii.gz, but is there error actually occurring
because I am not feeding in grad_dev.nii.gz via the -g option? Do I need a
newer version of FSL?
Thanks,
Derek Archer
From: Stamatios Sotiropoulos [mailto:[email protected]]
Sent: Monday, February 16, 2015 12:48 PM
To: Archer,Derek B
Cc: [email protected]<mailto:[email protected]>
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, Archer,Derek B
<[email protected]<mailto:[email protected]>> wrote:
Matt,
Thanks for the fast reply. I will use these three inputs in bedpostX.
Derek
From: Glasser, Matthew [mailto:[email protected]]
Sent: Monday, February 16, 2015 11:24 AM
To: Archer,Derek B;
[email protected]<mailto:[email protected]>
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
Not all of this may yet be available in the public release (you might need to
use --model=2 for now).
Peace,
Matt.
From: <Archer>, Derek B <[email protected]<mailto:[email protected]>>
Date: Monday, February 16, 2015 at 9:16 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
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/FNIRT, DTIFIT and probtrackx with this data?
>From what I've found in the archives, I need to do the following:
Bedpostx: include the -g option
FLIRT/FNIRT: do I include any extra options here?
DTIFIT: include the -gradnonlin option
Is this all that needs to be done to have this data ready for tractography? Or
are there steps that I have missed?
Please let me know if there is any documentation I have failed to locate.
Thanks,
Derek Archer
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