No, if usemaskanat = 1, then the diffusion mask that comes from applying
bet to the lowb volume will not be used for tractography. A dilated
version of aparc+aseg will be used as a mask instead, which is typically
more reliable than trying to find the right bet threshold.
On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:
Hi Anastasia
If I have T1 data available in my FS subject directory and I have
Use brain mask extracted from T1 image instead of low-b diffusion image?#
Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1
then will the B0 brain mask we spoke of below be used?
Deryk
On Fri, Jun 10, 2011 at 10:46 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Deryk - This variable is only used to average lowb images to
create a mask, so in your case you can set it to 2 and it'll
just use the first 2 volumes from your nii file. Sorry for the
confusion!
a.y
On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:
Dear Tracula Users
Does Tracula assume that the number of B0 scans, specified
in Step 7.3 of
the config file tutorial (below), are the first X number
of volumes in the
4Dnii.gz file or will the Tracula routines know from the
bvals file where
the B0 scans are ordered in the file? For example, I have
two runs of 16
directions + 2 B0s each for each of my subjects. I have
merged the two runs
together and the resulting file has the volumes ordered
such that the bvals
are entered into Tracula as follows:
0
0
1000
1000
1000
etc
0
0
1000
1000
1000
etc
My question pertains to the following part of the Tracula
config file:
Step7.3: Specifying Number Of low-b Images The last step
to set up if not
using original DICOMs would be to specify the number of
low-b images with
the following variable:
set nb0 = *No. of low-b images*
Thank you in advance for your help.
Cheers,
Deryk
Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
Speech-Language Pathologist
C.I.H.R. Post Doctoral Research Fellow
Department of Cognitive and Neural Systems Speech
Laboratory
Boston University, 677 Beacon Street, Boston, MA 02215
dsb...@bu.edu
http://blogs.bu.edu/dsbeal/about/
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