Hi Eileen - Have you checked the anatomical segmentations of the subjects?
The mask that's used by default is the aparc+aseg_mask, which comes from
registering the cortical parcellationg and subcortical segmentation from
T1 to diffusion space, and then dilating it by a couple of voxels.
If you upload an example data set for me here, I can take a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Please include all tracula-related directories of the subject (dmri,
dlabel, etc).
Thanks!
a.y
On Thu, 18 Dec 2014, Eileen Moore wrote:
Hi - I'm having difficulty with missing or incomplete tracts most of my
subjects. I'm hoping for suggestions on where I can look for data
problems. The majority of my subjects have at least one missing/incomplete
tract, but the specific problematic tract varies across
subjects (e.g., one subject has a missing L.Uncinate; another subject has a
missing Forceps Major; another is missing the ILF bilaterally,
etc.). For my problematic tracts, the path.pd.nii.gz is a single line/curve
rather than the diffuse volumetric distribution. I'm not
sure how to correct this.
I have checked my eigenvectors -- the lines appear to be pointing in the
correct directions in my dtifit_V1 -- so I believe my gradient
table is correct
I've checked my images for motion via visual inspection and by excluding any
subjects with dwi_motion outliers in AvgTranslation,
AvgRotation, PercentBadSlices, and AvgDropoutScore.
I inspected the nodif_brain_mask.nii.gz to look for chunks of missing brain
and did not identify any problems here.
I've tried increasing the number of control points for each tract.
I'd very much appreciate any suggestions on how to troubleshoot next.
Thank you,
Eileen.
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