Sorry, the b0dc.nii.gz should be the argument of --vsm (no need to use --exfdw).
On 09/12/2014 08:28 AM, Reza Rajimehr wrote: > 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? Both of those options are the same thing (I could not decide what to call it). > 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 ...? Actually, tkregister2 does not take a VSM, so you will be looking at the nondewarped. You can use mri_vol2vol with the --vsm option to map the template into anatomical space and unwarp, then load that up in tkmedit to see the surfaces on the dewarped. > > Finally what is the effect of specifying -b0dc in mkanalysis-sess? It just tells it to use the B0 distortion corrected data. > > 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 > > -- 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 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.
