try now On 3/21/16 10:24 PM, Bharadwaj, Pradyumna - (prad) wrote: > Hi Doug, > > Could you please upload epidewarp.fsl for FSL 5.x once again. > > Thanks! > -Prad > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > Sent: Tuesday, March 1, 2016 12:39 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] epidewarp.fsl for FSL 5.x > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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