Should the phase image be in rads? and does the magnitude image need to be skull-stripped first?
On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer <corinna...@gmail.com> wrote: > thanks Doug, I will give that a try. > > > On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> 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 < >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> > >>> >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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> >>> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: >>> https://gate.nmr.mgh.harvard.**edu/filedrop2<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> >>> >>> <http://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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >>> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 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<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >
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