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 <ayendiki@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