users > Unwarping EPI
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Apr 5, 2017 03:04 PM | Jason Liou
Unwarping EPI
Hello
I can't apply the computed deformation to diffusion-weighted image for creating an unwarped reformatted image.
My OS is Win7 64 bits . Unzip CMTK-3.2.2-Windows-x86 version with Windows Powershell(x86).
It is the procedure I do.
1)
I prepare four images which are NIFTI-format. Each of them is zipped in the .gz-format compressed file respectively and placed in the path \input
b0_rev.nii ---- reverse phase-encoded b = 1000
b0_fwd.nii ---- standard phase-encoded b = 1000
b1.nii ---- 1st diffusion image b = 1000
b2.nii ---- 2nd diffusion image b = 1000
And I input
./epiunwarp --write-jacobian-fwd epiunwarp\jacobian_fwd.nii input\b0_fwd.nii.gz input\b0_rev.nii.gz epiunwarp\b0_fwd.nii epiunwarp\b0_rev.nii epiunwarp\dfield.nrrd
After the processing is finished, the file "b0_fwd.nii.gz", "b0_rev.nii.gz", "dfield.nrrd" , "jacobian_fwd.nii.gz" appears in the path \epiunwarp
2)
However, after I input
./reformatx --floating input\b1.nii --linear -o epiunwarp\b1.nii epiunwarp\b0_fwd.nii epiunwarp\dfield.nrrd
it pops up the window "reformatx has stopped working", and there is not any new result in the path \epiunwarp
Is there any restriction of Unwarping EPI method or do I use it wrongly?
Thank You!
Jason
I can't apply the computed deformation to diffusion-weighted image for creating an unwarped reformatted image.
My OS is Win7 64 bits . Unzip CMTK-3.2.2-Windows-x86 version with Windows Powershell(x86).
It is the procedure I do.
1)
I prepare four images which are NIFTI-format. Each of them is zipped in the .gz-format compressed file respectively and placed in the path \input
b0_rev.nii ---- reverse phase-encoded b = 1000
b0_fwd.nii ---- standard phase-encoded b = 1000
b1.nii ---- 1st diffusion image b = 1000
b2.nii ---- 2nd diffusion image b = 1000
And I input
./epiunwarp --write-jacobian-fwd epiunwarp\jacobian_fwd.nii input\b0_fwd.nii.gz input\b0_rev.nii.gz epiunwarp\b0_fwd.nii epiunwarp\b0_rev.nii epiunwarp\dfield.nrrd
After the processing is finished, the file "b0_fwd.nii.gz", "b0_rev.nii.gz", "dfield.nrrd" , "jacobian_fwd.nii.gz" appears in the path \epiunwarp
2)
However, after I input
./reformatx --floating input\b1.nii --linear -o epiunwarp\b1.nii epiunwarp\b0_fwd.nii epiunwarp\dfield.nrrd
it pops up the window "reformatx has stopped working", and there is not any new result in the path \epiunwarp
Is there any restriction of Unwarping EPI method or do I use it wrongly?
Thank You!
Jason
Apr 8, 2017 05:04 AM | Torsten Rohlfing
RE: Unwarping EPI
Hi Jason -
Sorry for the delay.
At first glance, the command lines look reasonable. Just a few questions about your data:
You are saying,
b0_rev.nii ---- reverse phase-encoded b = 1000
b0_fwd.nii ---- standard phase-encoded b = 1000
but these should be b=0 images. Is that what you meant?
Also, are all the input images you are using the same resolution, matrix size (i.e., number of pixels), and the same slice orientation?
If the answer to each of the above is, yes, then I cannot think of anything obvious that is wrong here. In that case, maybe you could upload your images somewhere from where I could get them to take a look what exactly is happening?
Best,
Torsten
Sorry for the delay.
At first glance, the command lines look reasonable. Just a few questions about your data:
You are saying,
b0_rev.nii ---- reverse phase-encoded b = 1000
b0_fwd.nii ---- standard phase-encoded b = 1000
but these should be b=0 images. Is that what you meant?
Also, are all the input images you are using the same resolution, matrix size (i.e., number of pixels), and the same slice orientation?
If the answer to each of the above is, yes, then I cannot think of anything obvious that is wrong here. In that case, maybe you could upload your images somewhere from where I could get them to take a look what exactly is happening?
Best,
Torsten