If both phase and magnitude data are there, you could use fslroi to separate the images out into two separate files.

hth d

On 7/14/16 9:52 AM, Afzal, Afsana wrote:

Hi,

Just wanted to follow up on the issue of just having one fieldmap file for beta-zero correction outlined below.

Thanks for your help,

Afsana

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*Afsana Afzal* Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [AAFZAL@mgh.harvard.edu] *Sent:* Tuesday, July 12, 2016 2:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Beta-Zero Correction - No Phase File

Hi,

I'm working with a dataset that outputs only one file (not two separate mag and phase files) for the fieldmap. The data was also collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the fieldmaps are unpacking differently). I've attached the .dat file for one of the fieldmaps in this email.

If there a way to separate out the mag and phase from the single fieldmap file so I can use epidewarp.fsl?

Thanks,

Afsana

---

*Afsana Afzal* Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Hi Doug,

Thanks for getting back to me. I've tried mri_convert $Input_file --split $Output_file to split up the fieldmaps but I'm getting 6 to 12 different outputs (depending on the fieldmap) rather than just the mag and phase files which is what I was expecting.

Have you encountered this before and is there another way to unpack the fieldmaps into just the mag and phase components?

Thanks so much for you time,

Afsana

______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2016 12:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Beta-Zero Correction - No Phase File

You can extract frames from a multi frame file with mri_convert input.nii.gz --frame 0 output.frame0.nii.gz

On 07/12/2016 02:29 PM, Afzal, Afsana wrote:

Hi,

I'm working with a dataset that outputs only one file (not two separate mag and phase files) for the fieldmap. The data was also collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the fieldmaps are unpacking differently). I've attached the .dat file for one of the fieldmaps in this email.

If there a way to separate out the mag and phase from the single fieldmap file so I can use epidewarp.fsl?

Thanks,

Afsana

---

*Afsana Afzal* Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

---

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