MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-00001-000001-01.nii --dph /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-00001-000001-02.nii --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm fMRI/RPA003/bold/b0dcmap.nii.gz
> On Feb 10, 2016, at 22:58, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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 < >>> <mailto:gr...@nmr.mgh.harvard.edu>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 >>>> >>>> <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 >>> <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. >> >> -------------------------------------------------------------------------------- >> >> 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 <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 >> <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 > > > 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 Cell Phone: 202-297-8117 http://joedien.com
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