Hi Reza,
On Sep 6, 2014, at 13:47 , Reza Rajimehr reza@nmr.mgh.harvard.edu wrote:
I forgot to mention that I want to use undistorted EPI volumes for the functional-anatomical registration.
Well that is simple then, just undistorted the 3D EPI image you used as template for motion correction and register this tho the anatomical (if you have a surface recon for the anatomical I hear BBB is the registration method of choice). To overlay statistics result on the anatomical just use the the same “warp” as for the mock template and you should be fine.
Best Regards Sebastian
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 ...
How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an
example command would be very useful.
- How will the undistorted volumes be used later on in the FS-FAST
analysis stream?
Your help would be very much appreciated.
Thanks, Reza
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