Create the B0 voxel shift map. Call it b0dcmap.nii.gz and put it in
the bold folder, eg:

epidewarp.fsl \
 --mag mag.nii.gz \
 --dph dphase.nii.gz \
 --tediff YOUR_TE_DIFF --esp YOUR_ESP  \
 --vsm bold/b0dcmap.nii.gz

When you run mkanalysis-sess and preproc-sess, add "-b0dc" to the
command lines.

doug

On 05/03/2013 12:16 PM, Corinna Bauer wrote:

Yes, I am using FSFAST.

On Fri, May 3, 2013 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:


    Hi Corinna, are you using FSFAST? If not, are you still going to the
    surface?
    doug

    On 05/03/2013 11:07 AM, Corinna Bauer wrote:
    > Is there a way to correct fmri data for epi distortions in
    freesurfer?
    > Or does the data need to be first fun through FSL's B0 unwarping?
    >
    > Corinna
    >
    >
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    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center

    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

    Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/