Hi Doug, So I am using a command like this:
epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph ~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf ~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw ~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46 --esp 0.31 --sigma 2 --perev (note that instead of --o b0dc.nii.gz, I wrote --exfdw b0dc.nii.gz because this command apparently does not have --o option) Before running the above command, I have registered the mag and phasediff volumes to the template volume and I have generated new volumes (fid_mag and fid_phasediff) that are already in register with the template. I have two steps remaining in preproc-sess, which are register-sess and rawfunc2surf-sess. Should I use both -b0dc and -vsm flags for these two commands? I assume that when I use the above flag(s), my EPI fmc volumes will be dewarped first, and then they will get registered to the anatomical and the surface, right? So I hope that when I view/check the result of registration with tkregister2 (for possible manual interventions), I will see the dewarped template ...? Finally what is the effect of specifying -b0dc in mkanalysis-sess? Thanks, Reza > 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 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.
