Re: [HCP-Users] Processing Diffusion MRI Data

Glasser, Matthew Tue, 17 Feb 2015 09:59:21 -0800

Are you running the command on ${StudyFolder}/${Subject}/T1w/Diffusion ?

You’ll need the latest version of FSL 5.0.8 on your cluster as well.

Peace,

Matt.

From: <Archer>, Derek B <[email protected]>
Date: Tuesday, February 17, 2015 at 11:53 AM
To: Matt Glasser <[email protected]>, Stamatios Sotiropoulos <[email protected]>, "[email protected]" <[email protected]>
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 –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]>
Date: Tuesday, February 17, 2015 at 9:20 AM
To: Stamatios Sotiropoulos <[email protected]>, "[email protected]" <[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]
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]> 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]
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]>
Date: Monday, February 16, 2015 at 9:16 AM
To: "[email protected]" <[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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