Hi Ping - Thanks for the images. It looks like the initial path for
forceps major (which is chosen from the atlas) is not well-aligned with
your subject's forceps major (it's almost going into CSF). This could mean
that the registration between your subject and the atlas (MNI) is less
than pe
Glad things are moving in the right direction. Now it looks like maybe one
of the control points of the path is not moving around, which is why you
get that very bright thin spot in the distribution. I can't tell by
looking at that one slice of the mask only, but could it be that there
voxels
The mask sort of covers the whole brain (see attached). It may be due
to the display thresholding, when I viewed the path.pd.nii.gz using
fslview, the tract actually has been recovered as compared to the
previous one (old_path.png).
However, the path.pd still does seem normal, i.e. with quite a fe
Hi Ping - Do the corresponding brain masks in diffusion space
(dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz)
now cover the entire brain well, after the aparc+aseg fixes?
a.y
On Tue, 18 Oct 2011, Ping-Hong Yeh wrote:
Hi Anastasia,
I got fixed of the aparc+aseg (see
Hi Ping-Hong,
Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask
will be extracted from the DWI data by the bet tool, instead of using the
aparc+aseg.
But, and this is a big but, TRACULA uses the aparc+aseg to constrain the
tractography solutions, i.e. the aparc+aseg i
Hi Ping - You can upload your data if you want me to take a look at it.
1. The initial points ideally should be along the midline of the pathway,
starting from one end region of the pathway and going all the way to the
other end region. (The default number is 5 control points but you can "set
Hi Anastasia,
I've tried both options, the choice 1 fixed some of the cases, but
not all; and the choice 2 did not work at all. Maybe I've missed
something here.
Few more questions:
1. Will the initial points have to include the points around start,
way, and end points of the tracts need to be
Hi Ping - There are 2 possibilities:
1. You can try to fiddle with the initialization points yourself to make
sure they're well in the CST. The point coordinates are saved in a text
file - look at the --init argument of the dmri_paths command line, which
you can find in trac-all.log.
2. You c
Hi Priti,
Adjusting the threshold does not help. Indeed, the voxel number, only
about 50 or so, is much less compared to right cst, which has couple
thousands. In addition, the segmented image is a binary image, i.e.
only intensity 0 and 1000, while other tracts have gray scale ranging
from 0 to
Hi Ping - It looks like the path initialization may have failed. The
algorithm needs an initial guess for the path and iterates from there.
This initial guess is chosen based on the tracts in the atlas and if your
subject is not perfectly aligned with the atlas this initial guess might
end up
Hi Ping,
Did you try adjusting the threshold for left cst tract? In freeview you
can find the tract labels in the left corner, if you click on the left cst
tract and use the threshold button below to decrease the threshold. Please
let us know if that improves the visualization.
Cheers,
Priti
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