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 2012, Kiely Donnelly wrote:
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 I've never
seen before (I've attached a shot). I'm new to Freesurfer so I would
appreciate any help you may have.
Thanks again,
Kiely
On Tue, Jan 24, 2012 at 1:21 PM, Priti Srinivasan
<rspr...@nmr.mgh.harvard.edu> wrote:
Hi Kiely,
I had a similar experience with one of my subjects, but I
realized that
the original diffusion image had a lot of signal loss in various
regions
and hence the subsequent registration steps failed.
It can happen when either intra-subject or inter-subject
registration
fails. I would inspect the original diffusion image
(dmri/dwi_orig.nii.gz)
and the original anatomical (dlabel/anat_brain_mask.nii.gz) to
see if they
have any problems (signal loss etc) which could lead to failures
in
registration as a first step.
If both your diffusion and anatomical are both good, then I'd
try to do
flirt seperately to see if you get the same results as the one
produced by
tracula.
Hope this is helpful,
Priti
> 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 me with a different problem I ran
into. For
several of our subjects, each pathway reconstruction fails and I
get an
error like the following for all 18 tracts:
>
> Processing pathway 16 of 18...
> Initializing MCMC
> INFO: Path from initial control points is not entirely in mask
> INFO: or is self-intersecting
> INFO: Attemping to perturb control points
> ERROR: Path from initial control points is not entirely in
mask
> ERROR: or is self-intersecting
> ERROR: Initialization failed
> ERROR: Pathway reconstruction failed
> Done in 0.216 sec.
>
> I am able to view the FA image in native space, but when I
attempt to
view
> the FLIRT-registered FA image it's completely dark. Is there
any reason you
> can think of that this may be happening?
>
> Thanks in advance,
>
> Kiely
>
>
> On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
>
>> 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 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 seemed to work (I no longer
received the
message "1 slice processed" over and over), but for some reason
the
merged_ph1samples.nii.gz file is still not being created and I
continue to run into an error when I run -path. It does create a
merged_ph2samples.nii.gz output file.
>>> Any help would be greatly appreciated.
>>> Thanks,
>>> Kiely
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>
> --
> Kiely M. Donnelly, M.A.
> Doctoral Candidate, Clinical Neuropsychology
> University of Cincinnati
> _______________________________________________
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--
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati
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