Stam missed something in this e-mail:
2. You don’t want to be using --invxfm
if you are specifying a simple affine (use --xfm). --invxfm is only for
when you specify a warpfield. In that case, you specify the forward warp
with --xfm and the inverse warp with --invxfm.
Correcting this should solve your problem
in 3.
Peace,
Matt.
From:
Sent: Friday, August 12, 2011 4:44
AM
To: [log in to unmask]
Subject: [FSL] Fw: Problems when
using probtrackx
[I
made a mistake in the last mail and now corrected. Sorry!]
Hi,all~
I
came across 4 questions when using the probtrackx from FSL:
1. Will
adding Waypoint masks, or Exclusion mask, or Termination mask have an effect on
the value of
voxels in the fdt_paths.nii.gz, if the same seed mask and target mask are used?
2.
Flirt to register DWI to MRI and MRI to MNI152, and get two transformation
matrix, and concat them to get a matrix M. Then I probtrackx with the option --invxfm.
I want to verify if there is something wrong when adding the concated transform
matrix?
3.
Are the output volume fdt_paths.nii.gz is in the space of the masks? I want to
confirm since my output file is not, through I saw the FSL
webpage says yes. I think I may do somethin wrong, say, the problem
2.
4.
How can I only get the tract connecting the seed and target mask since
there are so non-zero
voxels in the volume fdt_paths.nii.gz?
Waiting
for your valuable advice!
2011-08-12
Xiangzhen Kong