On 09/06/2014 07:10 AM, Reza Rajimehr wrote: > Hi, > > I have a basic question, but the answer can be useful for others as well. > > I am doing a customized preprocessing of monkey functional data in FS-FAST > v5.3. After motion correction and before functional-anatomical > registration, I want to use fieldmap data to correct spatial distortions > of EPI data. So: > > My fieldmap data: dicom files from a fieldmap scan (there are actually two > series of dicom files for that scan) > > My EPI data: fmc.nii.gz files in run folders > > Now I have three questions: > > 1) How can I unpack the fieldmap data? An example command ... I think you get two series out, one magnitude and one phase, just convert those to nifti > > 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an > example command would be very useful. something like epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o b0dc.nii ... You have to add --tediff and --esp, but those depend on you sequence Put the output (b0dc.nii) into session/bold (or session/rest, or where ever your fmri data are located) > > 3) How will the undistorted volumes be used later on in the FS-FAST > analysis stream? When you run preproc-sess and mkanalysis-sess add -b0dc to the command line
> > Your help would be very much appreciated. > > Thanks, > Reza > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] 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.
