Re: [Freesurfer] epi correction of fmri data

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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.