dke-questions > ordering of bvecs
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Mar 19, 2019 01:03 PM | Corinna Bauer
ordering of bvecs
Hello all,
I have 30 direction DKI data at b1000 and b2000 with a single b0. The b0 is at the beginning of the dataset, which then alternates back and forth between the b1000 and b2000. My question is regarding the btable and the ordering of the data. Do I need to reorder the data so that all the b1000 images come first, followed by all the b2000 images, or is it acceptable to keep them as alternating. The bvecs in the gradient table are currently alternating (b1000, 2000, 1000, 2000, etc.) to match the images.
Thank you
Corinna
I have 30 direction DKI data at b1000 and b2000 with a single b0. The b0 is at the beginning of the dataset, which then alternates back and forth between the b1000 and b2000. My question is regarding the btable and the ordering of the data. Do I need to reorder the data so that all the b1000 images come first, followed by all the b2000 images, or is it acceptable to keep them as alternating. The bvecs in the gradient table are currently alternating (b1000, 2000, 1000, 2000, etc.) to match the images.
Thank you
Corinna
Mar 19, 2019 09:03 PM | David Lewis - Medical University of South Carolina
RE: ordering of bvecs
Hi Corinna,
Is the data in Nifti format or Dicom? If the data are in a 4D Nifti file, the data ordering has to be the b0 volume followed by all the b1000 volumes and then followed by all the b2000 volumes. If the data are Dicom images in a directory, I don't know if the order matters but I can look into it.
Best,
Dave
Is the data in Nifti format or Dicom? If the data are in a 4D Nifti file, the data ordering has to be the b0 volume followed by all the b1000 volumes and then followed by all the b2000 volumes. If the data are Dicom images in a directory, I don't know if the order matters but I can look into it.
Best,
Dave
Mar 19, 2019 09:03 PM | Corinna Bauer
RE: ordering of bvecs
Hi Dave,
Thank you for your reply. It is in Nifti format, so I'll reorder the volumes and the bvecs to be the b0 volume, all the b1000 volumes, and then all the b2000 volumes.
Thanks
Thank you for your reply. It is in Nifti format, so I'll reorder the volumes and the bvecs to be the b0 volume, all the b1000 volumes, and then all the b2000 volumes.
Thanks
Mar 20, 2019 12:03 PM | David Lewis - Medical University of South Carolina
RE: ordering of bvecs
Hi Corinna,
Glad I could help and thanks for using DKE!
Dave
Glad I could help and thanks for using DKE!
Dave
Mar 20, 2019 08:03 PM | Corinna Bauer
RE: ordering of bvecs
> Thanks Dave,
>
I have one further question, I noticed that the kfa map looks a little
noisy for my test subject from our patient group (ventriculomegaly with
periventricular white matter damage). I have run DKE using both weak and
strong filtering and there is an obvious difference, but I am not sure
which is best to use. Would be able to take a quick look and let me know
which one looks better to use moving forward? Both have been run with the
background threshold of 20.
dki_kfa_T20_filter2.nii
dki_kfa_T20_filter1.nii
Thanks!
Corinna
>
I have one further question, I noticed that the kfa map looks a little
noisy for my test subject from our patient group (ventriculomegaly with
periventricular white matter damage). I have run DKE using both weak and
strong filtering and there is an obvious difference, but I am not sure
which is best to use. Would be able to take a quick look and let me know
which one looks better to use moving forward? Both have been run with the
background threshold of 20.
dki_kfa_T20_filter2.nii
dki_kfa_T20_filter1.nii
Thanks!
Corinna
Mar 20, 2019 08:03 PM | Corinna Bauer
RE: ordering of bvecs
Sorry, it looks like the images didn't attach properly. Here is
filter 2