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Subject:

Fieldmaps with flirt BBR

From:

Jordan Poppenk <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 10 Apr 2013 22:04:47 +0100

Content-Type:

text/plain

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text/plain (54 lines)

Dear FSL experts,

When using my fieldmaps with BBR, I find that they have no effect. I am having trouble diagnosing the problem, and wondered whether one of you might be able to offer some advice. I am basing my pipeline off of the contents of epi_reg.

I currently get an error that suggests there is a conversion problem (see step 3d below), which suggests to me that I have somehow gone wrong in preparing my images, rather than this being a problem with BBR.

Consistent with this interpretation, things also go awry when I attempt to create a warp image. I have described my pipeline below along with brief descriptions of the associated images at each step.

Any help would be much appreciated!

Cheers,
Jordan



1. I am starting with a fieldmap image that looks good visually (mostly grey in the brain area with a white patch in vmPFC), and where voxels have the range -1277 to +1277. 

2. I apply fugue to create an unmasked image that also looks good with the same intensity range:
fugue --loadfmap=fmap --mask=fmap_mask --unmaskfmap --savefmap=fmap_unmasked --unwarpdir=y-


** BBR application ***

3a. I use applywarp to transform this image to the subject's T1 anatomical (using a transform derived elsewhere). This still look sgood.

3b. I use fslmaths to obtain an inner mask

3c. I use fugue to create a dilated version of the file that still looks good. I end up with a range -1277 to +1277:
fugue --loadfmap=fmap_anatomical --mask=innermask --unmaskfmap --unwarpdir=y- --savefmap=fmap_dilated

3d. Using flirt and BBR, I complete registration with no fieldmap:
flirt -ref T1_anat -in epi -dof 6  -cost bbr -wmseg anat_wm -init prelim_xfm -omat func2anat.mat -out test_output_nofmap -schedule ${FSLDIR}/etc/flirtsch/bbr.sch

3e. ...and then with fieldmap:
flirt -ref T1_anat -in epi -dof 6  -cost bbr -wmseg anat_wm -init prelim_xfm -omat func2anat.mat -out test_output_fmap -schedule ${FSLDIR}/etc/flirtsch/bbr.sch -echospacing 0.00039 -pedir y- -fieldmap fmap_dilated
** this produces the text,
"Warning: Out of range or non-integer values truncated during conversion to character"

3f. I compare the images and see no difference anywhere in the brain when toggling between test_output_fmap and test_output_nofmap


** Unwarp application **
4a. I use applywarp to align my fieldmap with my epis (still in the range -1277 +1277)

4b. I make a mask with fslmaths

4c. I use fugue to create a "shift" image with range of about -6 to +6 (still looks like a fieldmap):
fugue --loadfmap=fmap_coreg --mask=epi_mask --saveshift=fmap_shifted --unmaskshift --dwell=0.00039 --unwarpdir y-

4d. I use convertwarp to create a dewarp image, but this yields nothing but a big gradient from R to L (intensity range 0 to 2), (which is especially weird given that I have been specifying A>P all along):
convertwarp -r epi -s fmap_shifted -o warp_img --shiftdir=y- --absout

4e. I use applywarp to apply the warp image to an epi and get the error, "an error occurred while reading file: fmap_shifted

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