It needs to be 0 to 4095, see below --ph phasevolid
Phase volume from the B0 fieldmap (if the phases from Echo1, Echo2 are available instead of their difference). These are assumed to be scaled between 0 to 4095 for -pi to pi. Eg, ph.ext, where ext is either nii, nii.gz, or img. Not with --complex or with --dph. This is made to work with the default Siemens field map. Note that you can also use complex inputs instead of mag and phase doug On 05/03/2013 01:05 PM, Corinna Bauer wrote: > 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 > <mailto: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 <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel: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> > 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> > > <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> > <mailto: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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto: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> > 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/ > > > -- 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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
