Unfortunately I'm not allowed to share these files without direct IRB approval 
(even if they are anonymized). I just tried on some Siemens TrioTim data with 
the same results.

Graham
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 2:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dcm2niix

Can you upload the dicoms so I can test it out? filedrop address below


On 02/08/2017 02:13 PM, Warner, Graham Cary wrote:
> The set I'm look at now was collected on a GE Signa HDxt.
>
> Graham
> ------------------------------------------------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 2:09 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> What scanner(s) was it acquired on?
>
> ------------------------------------------------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham
> Cary [gwar...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 2:07 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> I'm using a large dataset from mi2b2 which contains data from multiple
> vendors/models collected at different hospitals in the partners
> network between 2003 and 2016. The data I tried running mri_convert on
> was acquired in 2011.
>
> Graham
> ------------------------------------------------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 1:55 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> Old versions of mri_convert (before 6.0) used to output a default
> Siemens gradient table - this was not read from the header of the
> dicom file itself. The 6.0 version reads the table from the header, as
> long as it is a relatively modern dicom file that has the table in a
> standard position in the header. When/where was your data acquired?
>
> ------------------------------------------------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham
> Cary [gwar...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 1:21 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> I just tried it on a few and while it was able to generate the nii
> files it failed to generate the bval/bvec files I'm looking for. Is it
> not typical behavior for mri_convert to generate bval/bvec files for
> DTI runs or is this an error?
>
> Graham
> ------------------------------------------------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 10:15 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> Hi Graham – Have you tried mri_convert? The 6.0 version should be able
> to extract diffusion gradient tables and b-value tables from most
> standard recent dicoms.
>
> a.y
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Warner,
> Graham Cary" <gwar...@mgh.harvard.edu <mailto:gwar...@mgh.harvard.edu>>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Wednesday, February 8, 2017 at 10:01 AM
> To: "freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>"
> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] dcm2niix
>
> Hi all,
>
> Can we get dcm2niix added to the system instance of fsl? It can't find
> it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and
> I'm just not seeing it). I'm having problems generating .bval and
> .bvec files from certain DTI datasets using dcm2nii and the NITRC guys
> told me I should be using dcm2niix.
>
> Thanks,
> Graham