Dear Graham,

you could also try mrconvert of mrtrix3. This tool is very useful and has very good support.

http://mrtrix.readthedocs.io/en/latest/reference/commands/mrconvert.html

community.mrtrix.org

Regards,

Antonin

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?

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*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?

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*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