try now On 03/01/2016 02:16 PM, Versace, Amelia wrote: > > Hi, > > I am having the same issue. > > Can you please upload the updated version of epidewarp.fsl for FSL 5.x. > > Thanks a lot, Amelia > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas > Greve > *Sent:* Wednesday, February 10, 2016 10:58 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] epidewarp.fsl for FSL 5.x > > what is your command line? I think there is a rescaling in which it > expcts the phase to be 0-2048 (or 4096) as this is how it comes of the > (siemens) scanner. Could that be the problem? > > On 2/10/16 10:40 PM, Joseph Dien wrote: > > I ran into the same issue: > > FSLVersion 5.0.4 > > FSLVerMaj 5 > > FSL Version is 5.0.4, must be 3.X or 4.X > > I downloaded the epidewarp.fsl script from the suggested ftp site > and replaced the existing script. It did indeed fix the version > incompatibility with FSL 5.x. > > I ran into a new problem where it was aborting. After some > trouble shooting and looking over the documentation, I realized > that —-epi is a required input without which the script crashes > (or is it supposed to be optional but there is a bug in the script?). > > After including it, it ran much further but then aborted with the > following error: > > ERROR: input phase image exceeds allowable phase range. > > Allowable range is 6.283 radians. Image range is: 12.5633 radians. > > This is consistent with the documentation. I’m not sure why the > phase image exceeds the range though. > > It ran without problems with SPM’s FieldMap Toolbox and it is from > a standard Siemen’s scanner sequence (two magnitude files and one > phase difference file). > > Do I just divide the values by two with something like fslmaths > since it seems to have exactly double the required range? > > Joe > > On Nov 26, 2014, at 21:36, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > wrote: > > > It is there again. I don't know what the status if it is in > terms of the version. Try it and let me know > doug > > On 11/25/14 4:34 PM, Morgan Hough wrote: > > Hi Doug, > > Could you put the epidewarp.fsl script back on your ftp > site? I don’t see it at the link in the archives: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl > > BTW, is the script updated in some way for 5.x or can I > can the old script just be changed to accept 5.x version > numbers. > > Cheers, > > -Morgan > > _______________________________________________ > 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. > > > -------------------------------------------------------------------------------- > > Joseph Dien, PhD > > Senior Research Scientist > > Maryland Neuroimaging Center > > University of Maryland, College Park > > E-mail: jdie...@mac.com <mailto:jdie...@mac.com> > Cell Phone: 202-297-8117 > http://joedien.com > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > 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 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
