Dear Jesper,
 
  I've uploaded the fieldmap.nii under reference number 530027. I used the FEAT GUI to do the B0 correction and it asked for both the EPI's TE (30ms) as well as the echo spacing/dwell time.  My protocol's echo spacing was .8ms; however, I'm using Grappa with an acceleration factor of 2, so the effective echo spacing should be .4ms, I think. The difference between TEs in the B0 acquisition was 2.58.  Thanks again!
 
Best,
 Steven
 
p.s. I also included the code I used to generate the fieldmaps below:
 
 
%# Convert Phase images to radians. Move orig phase 1 and 2 to raw dir.
system('fslmaths b0mapping/b0quants/b0_phase1.nii.gz -mul 3.141529 -div 4096 -add 3.141529 b0mapping/b0quants/phase1_rad.nii.gz -odt float');
system('fslmaths b0mapping/b0quants/b0_phase2.nii.gz -mul 3.141529 -div 4096 -add 3.141529 b0mapping/b0quants/phase2_rad.nii.gz -odt float');
 
%# Unwrap the phase images
system('prelude -a b0mapping/b0quants/b0_mag.nii.gz -p b0mapping/b0quants/phase1_rad.nii.gz -o b0mapping/b0quants/phase1_unwrapped_rad.nii.gz -m b0mapping/b0quants/b0_mag_bet');
system('prelude -a b0mapping/b0quants/b0_mag.nii.gz -p b0mapping/b0quants/phase2_rad.nii.gz -o b0mapping/b0quants/phase2_unwrapped_rad.nii.gz -m b0mapping/b0quants/b0_mag_bet');
 
%# Get the fieldmap in radians
system('fslmaths b0mapping/b0quants/phase2_unwrapped_rad.nii.gz -sub b0mapping/b0quants/phase1_unwrapped_rad.nii.gz -mul 1000 -div 2.58 b0mapping/b0quants/fieldmap_rads.nii -odt float');

On Tue, Jun 5, 2012 at 12:02 PM, Jesper Andersson <[log in to unmask]> wrote:
Dear Steven,

there is definitely something strange going on. 

Can you please also upload the data (fieldmap data) that was used to create these, along with the necessary extra info (echo time difference and dwell time). It looks like there might have been a problem with the phase unwrapping, but I cannot really say for certain from just the shift map.

Jesper

On 5 Jun 2012, at 16:02, Steven Marchette wrote:

Dear Jesper,
 
   Sorry about that, I didn't realize that the upload portion existed!  I'll keep to responsible bandwidth use in the future.  The reference number for my shift map nifty is 731176. Thank you again!
 
 Best,
  Steven

On Tue, Jun 5, 2012 at 10:53 AM, Jesper Andersson <[log in to unmask]> wrote:
Dear Steven,

 I just realized that our reply to you was confusing!  I was on Andrew's computer when we responded to you, and so the response bears his name also. He's been helping me on this a lot, but I wanted to let you know that his post contained the relevant info for my b0 correction issue.  Let me know if this was what you needed!


I see. I thought that was the case. When I asked you to send those images I meant using our upload service http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi to upload the actual nifti images. It is hard to say much from just seeing a jpg. Also, in general we discourage from sending pictures to everyone on the mailbase (for bandwidth reasons).

So if you could please upload the images (nifti) to there and email me the reference number when you have done that.

Jesper


 

 Best,

  Steven

On Fri, Jun 1, 2012 at 2:01 PM, andrew Persichetti <[log in to unmask]> wrote:

Hi Jesper,

Below is the shift map that shows the distortion oin the IPL (note the value of -13), in addition I've included fsl's firefox output images from the b0 correction portion of feat. The spike in the right most braion of the undistorted example seems top line up exactly with the light blue spot in the unwarping shift map. Let me know if you need anything else. Thanks!