Hi Moises,
thanks for quick reply. It's 5.0.7. I am not sure if I can upgrade to
the newest version (the institute where I am working decides that).
Pavel
On 26 November 2015 at 13:15, Moises Hernandez <[log in to unmask]> wrote:
> Hi Pavel,
>
> What version of FSL are you using ?
>
> Moises.
>
> On 26 November 2015 at 11:57, Pavel Hok <[log in to unmask]> wrote:
>>
>> 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
>>
>> --
>>
>> -------------------------------------------------------------------------------
>> -- MUDr. Pavel Hok
>>
>> -------------------------------------------------------------------------------
>> -- Laboratoř funkční magnetické rezonance
>> -- Neurologická klinika
>> -- Lékařská fakulta
>> -- Univerzita Palackého v Olomouci
>> -- Fakultní nemocnice Olomouc
>>
>> -------------------------------------------------------------------------------
>> -- Laboratory of functional magnetic resonance imaging
>> -- Department of Neurology
>> -- Faculty of Medicine and Dentistry
>> -- Palacky University Olomouc
>> -- University Hospital Olomouc
>> -- Czech Republic
>>
>> -------------------------------------------------------------------------------
>> -- I.P. Pavlova 6, 775 20 Olomouc
>> -- web: fmri.upol.cz
>> -- tel.: +420 588 443 418
>> -- e-mail: [log in to unmask]
>>
>> -------------------------------------------------------------------------------
>
>
--
-------------------------------------------------------------------------------
-- MUDr. Pavel Hok
-------------------------------------------------------------------------------
-- Laboratoř funkční magnetické rezonance
-- Neurologická klinika
-- Lékařská fakulta
-- Univerzita Palackého v Olomouci
-- Fakultní nemocnice Olomouc
-------------------------------------------------------------------------------
-- Laboratory of functional magnetic resonance imaging
-- Department of Neurology
-- Faculty of Medicine and Dentistry
-- Palacky University Olomouc
-- University Hospital Olomouc
-- Czech Republic
-------------------------------------------------------------------------------
-- 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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