This is the wrapper script that it’ll call, the input formats are explained here:

http://surfer.nmr.mgh.harvard.edu/fswiki/epidewarp.fsl

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of VA Research <n.n.di.methyl.tryptamine1@gmail.commailto:n.n.di.methyl.tryptamine1@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, March 22, 2017 at 2:29 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [FSL or FREESURFER] SIEMENS FIELDMAP B0 UNWARPING FOR DTI

do I have to prepare the mag file and make it radians/s for FreeSurfer?

like you do in FSL? with command fsl_prepare_fieldmap

On Wed, Mar 22, 2017 at 7:35 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Joseph – You can use fugue as part of the preprocessing in TRACULA. Search for items with “b0” in the example config file: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

Best, a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of VA Research <n.n.di.methyl.tryptamine1@gmail.commailto:n.n.di.methyl.tryptamine1@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, March 21, 2017 at 9:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, FSL - FMRIB's Software Library <FSL@jiscmail.ac.ukmailto:FSL@jiscmail.ac.uk> Subject: [Freesurfer] [FSL or FREESURFER] SIEMENS FIELDMAP B0 UNWARPING FOR DTI

Hello FSL and FS pros,

I am trying to pre process DW images but am not sure how to unwarp images.

We are using Siemens Skyra 3T and output fieldmaps;

2 files output from the scanner; the first file contains two magnitude files in one the second file contains the single phase difference image

------------------------------------------------------------------------------------------------------- FSL -------------------------------------------------------------------------------------------------------

through FSL we have run eddy correct, bet the magnitude file, and run fsl prepare fieldmap (example code below)

I am not sure how to use the prelude and FUGUE command and am unclear on their inputs/outputs

Does anyone in FSL land have a clear tutorial of how to utilize these tools?

for example, given my type of fieldmaps do i need to use prelude?

later through FSL stream we would like to complete bet preprocessed DW images, dtifit, bedpostx

---------------------------------------------------------------------------------------------------- FREESURFERS ---------------------------------------------------------------------------------------------------- I have read over the TRACULA requirements and how to edit the configuration files.

There is mention of eddy current correction that is available through tracula but nothing mentioned for dealing with the warping issue.

Does anyone in freesurfer land have any suggestions on how to tackle this as a part of the tracula data stream?

Any input will be appreciated, Thanks so much

Joseph Veliz Brentwood Biomedical Research VA Hospital West Los Angeles

---------------------------------------------------------------------------------------------------- example ---------------------------------------------------------------------------------------------------- #Eddy correction eddy_correct ${name}_dti.nii.gz /Users/seahorse/Studies/NN/DTI/${name}/${name}DTI_eddy.nii.gz 0

#BET fieldmap mag super tight; exclude all non brain voxels bet 10001_dtiFMmag1mag2.nii.gz /Users/seahorse/Studies/NN/DTI/10001/10001dtimags_brain.nii.gz -F -m -f 0.85

#generate fieldmap in rad/s for FEAT or FUGUE fsl_prepare_fieldmap SIEMENS 10001_dtiFMphase.nii.gz 10001dtimags_brain.nii.gz fmap_rads 2.46

#Prelude prelude -c data --unwrap=result prelude --complex=data -u result

#FUGUE Utility for Geometrically Unwarping EPIs; performs unwarping of an EPI image based on fieldmap data fugue -i epi -p unwrappedphase --dwell=dwelltime --asym=asymtime -s 0.5 -u result fugue -i epi --dwell=dwelltime --loadfmap=fieldmap -u result

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