Dear FSL experts,
I recently started to use FreeSurfer pial surface as my termination
mask in the ProbtrackX. The surface is continunuous and I had it
transformed to GIFTI format. Although the voxel values in fdt_paths
seem to drop abruptly (from e.g. 100) at the cortical surface, there
are still many fibres magically passing through the mask outside of
the brain. Most of them does not survive my thresholding (since the
values are between 1 and 5), but those close to my subcortical seed
actually will (since there are approx. 500 of them). In total, I run 2
million fibres from a single voxel mask sampled within a sphere of 1.5
mm radius and I made sure that this area is entirely within the brain.
This would not explain why the fibres jump through the surface in
other brain areas anyway.
Simply masking the fibres out is not a solution for me since I need
all the fibres starting in the wrong direction (i.e. towards the
cortical surface) to stop immediately in order to be discarded by
minimum distance threshold.
Any idea why this is happening and how can I prevent that?
Thanks for your help!
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
-- e-mail: [log in to unmask]
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