Saad,
No worries! I also thought my last e-mail might have been interpreted as not
needing a reply. =]
I didn't actually know there was a symmetric mode (might have made my script
writing easier!). What I am doing is running one probtrack from mask A to
mask B, then another from mask B to mask A.
For example, here are some lines from the scripts I have written:
probtrackx --mode=seedmask -x RInsula_4D.nii.gz -l -c 0.2 -S 2000
--steplength=0.5 -P 15000 --forcedir --opd -s ../merged -m
../nodif_brain_mask --dir=../../tracts/RInsula_4D_to_RPCG_2D-1
--waypoints=RPCG_2D.nii.gz --stop=RPCG_2D.nii.gz
and going the other way
probtrackx --mode=seedmask -x RPCG_2D.nii.gz -l -c 0.2 -S 2000
--steplength=0.5 -P 15000 --forcedir --opd -s ../merged -m
../nodif_brain_mask --dir=../../tracts/RInsula_4D_to_RPCG_2D-2
--waypoints=RInsula_4D.nii.gz --stop=RInsula_4D.nii.gz
Thanks,
Carlos
>Hi Carlos
>Sorry, I didn't realise you were waiting for a reply!
>
>In your last email, you said you were using the symmetric mode, are
>you using the gui for that? if not, are you using --mask2 or --network?
>and in both cases, which mask are you using as a termination?
>(if your seed mask is also a termination mask, then no tracts can go
>out of it!)
>
>Saad.
>
>
>On 16 Feb 2009, at 15:47, Carlos Faraco wrote:
>
>> Saad,
>>
>> Have you been able to find a reason for this? Would it help if I
>> sent my
>> masks and results over to you?
>>
>> Thanks,
>>
>> Carlos Faraco
>>
>
>Saad Jbabdi
>Oxford University FMRIB Centre
>
>JR Hospital, Headington, OX3 9DU, UK
>+44 (0) 1865 222545 (fax 717)
>www.fmrib.ox.ac.uk/~saad
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