Dear FSL experts,
I am quite new to analysing DTI data using probtrackX. I would be
grateful if you could provide me with some comments on the following:
I would like to compare fibre tracts from adjacent cortical seeds
(spheres of 5 mm in diameter in structural space). I am worried about
the streamlines going from the seeds in unpredictable directions
within the GM, possibly inducing false positive results (jumping over
sulci etc.). To overcome that I thought of couple of solutions, also
inspired by the mailing list:
- projecting the seeds on white matter surface (obtained by blurring
the segmentated WM mask with 3x3x3 kernel and thresholding it between
0.5 and 0.83) to get seed in approx. 1-voxel juxtacortical layer
- constraining the fibre tracking by WM mask with the cortical seed
mask added on top of it (the whole mask would be inverted to create an
exclusion mask)
- drawing an exclusion mask around the seeds in the gray matter
Which of those would make more sense? Using whole-brain WM mask seems
to be less user-dependent, but my diffusion-to-structural FLIRT
transformation matrices are far from perfect (due to distorsions). I
am trying FNIRT to register nodif_brain or FA map, but I have not the
results of those tests, yet.
Additionally, can I compare two fdt_paths files by just subtracting
them using fslmaths (provided they are normalised for the seed
volume)? Is there a way to assess the significance of the differences
(t-test)? I also thought of visualising the fibres by projecting them
on the brain surface when they reach GM.
Thanks for any hints!
Pavel
--
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-- MUDr. Pavel Hok
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-- Laboratoř funkční magnetické rezonance
-- Neurologická klinika
-- Lékařská fakulta
-- Univerzita Palackého v Olomouci
-- Fakultní nemocnice Olomouc
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-- Laboratory of functional magnetic resonance imaging
-- Department of Neurology
-- Faculty of Medicine and Dentistry
-- Palacky University Olomouc
-- University Hospital Olomouc
-- Czech Republic
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-- I.P. Pavlova 6, 775 20 Olomouc
-- web: fmri.upol.cz
-- tel.: +420 588 443 418
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