How to use DICOMDIR format

[刘政]

Hi

    The DTI data I've got is from Siemens 3T MRI scanner, and the data it gives me is in DICOMDIR format, which contains a lot of series. I used A software called MiscroDICOM to open it, and there are several series, 

Does anyone know which one I should use for VEP?

Thank you,

Barry

[WOODMAN Michael]

Hi

You would use the t1_mpr (and maybe the t2_spc)  for FreeSurfer and the ep2d_DTI for the diffusion part.  The important step is to check the sequence contains the gradient information, which can be done with mrinfo command from MRtrix3.

cheers,

Marmaduke

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Subject: [TVB] How to use DICOMDIR format

 

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[刘政]

Hi

    When you say gradient information, does itmena like this. When I open the DTI of ep2d_DTI series, there are 62 figures with 1024 * 2014 size, and in each figure, there're 8*8=64 brains in it. Like this

And do you know some tools that would help me trnasfer the DICOMDIR file to DICOM format, the software I am using now can do this, but if I use mrinfo to see the info of the dcm file transfered from the MiscroDICOM viewer, it gives me error like this

Thank you

Barry

[WOODMAN Michael]

hi

This would be the right series, but if MRtrix3 cannot read it, then you would need to find a converter to a format that it can read, perhaps nifti?

I can't help further, sorry, and please refrain from posting personal image data to the mailing list.

cheers,

Marmaduke

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From: tvb-...@googlegroups.com <tvb-...@googlegroups.com> on behalf of 刘政 <lz02...@gmail.com>

Sent: Wednesday, May 26, 2021 10:00:37 AM
To: TVB Users
Subject: Re: [TVB] How to use DICOMDIR format

 

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[刘政]

Hi

  Got it! And I just converted that series to nii.gz format, and use mrinfo command, get this

Is this the right output?

Thank you

Barry

[WOODMAN Michael]

Hi

That looks good except you will need the gradient information in addition to the nifti image. Frequently this is provided in a FSL convention with two files bvecs and bvals. lease refer to MRtrix documentation for more information .

Cheers

Marmaduke

> On 26 May 2021, at 13:32, 刘政 <lz02...@gmail.com> wrote:
>
> 

> Hi
>
> Got it! And I just converted that series to nii.gz format, and use mrinfo command, get this

[刘政]

Hi 

May I ask that how do you guys get the weight.txt, aka the weight matrix, with T1 MRI and DTI(T1 is a .nii.gz file, and DTI consisting of .nii.gz bvec bval)? I saw two repositories here https://github.com/the-virtual-brain/tvb-recon and https://github.com/ins-amu/scripts/tree/v0.4-CH. They all look working. And as to the Scripts, it has many tags, any recommendation? 

Thank you

Barry

[刘政]

Hi 

And is the parcellation optional, for I notice a new atlas called VEP-atlas

Thank you 

Barry

[刘政]

Hi all

I am using tvb-recon(https://github.com/the-virtual-brain/tvb-recon) docker image to get the weight.txt of structural  construction.

And I met this error: