Hi Priti,
Thanks for your help. I took another look at the original diffusion and
anatomical images. The anatomical looks OK, but in the diffusion image a
posterior region of the brain appears cutoff and when I view the image in
freeview there is a green box in the lower left hand corner that
Hi Kiely - If part of the brain is cut off in dwi_orig.nii.gz, it means it
was cut off in your original dicom. If there's actualy part of the brain
missing in all the volumes in your diffusion series, you may not be able
to reconstruct tracts that go through that part.
a.y
On Fri, 10 Feb
Hi Anastasia,
Sorry for my slow reply. I am working with data that I only have access to
intermittently. We were able to fix the problem by deleting the original
files from the folder and re-running the bedpost step. The old files must
have been interfering in some way.
I am hoping you can help
Hi Kiely - It's strange that bepostx would create ph2samples and not
ph1samples. These are the orientation angles for the 2 anisotropic
compartments, so if there's a 2nd there should be a 1st. Have you asked
about it on the FSL list?
a.y
On Thu, 22 Dec 2011, Kiely Donnelly wrote:
Hi
Hi Everyone --
I've been having difficulty getting Tracula to run smoothly on our cluster.
Similar to others on the listserv, the bedpost step was not creating the
necessary files causing an error during the -path step. Based on previous
posts, I ran bedpostx on the dmri directory. This initially
