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:
- 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
- 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)
- 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