aah! so there is no way of knowing whether or not each streamline has
been rejected, hence the difficulty at this point in knowing by how
much we're undershooting with waytotal, right? The 50% underestimation
that we've been talking about basically assumes that both ways are
always successful in finding a path?
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Cherif P. Sahyoun HST-MEMP
Developmental Neuroimaging of Cognitive Functions
C: 617 688 8048
H: 617 424 6956
[log in to unmask]
"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
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On Fri, Nov 28, 2008 at 2:55 PM, Dave Flitney <[log in to unmask]> wrote:
> Sorry. It doesn't actually have to do with randfib.
>
> The problem is: streamlines are tracked both ways from each voxel but only
> counted once. If the first half is rejected the second half is not counted
> even if it reaches a waypoint! This has been corrected and a patch will be
> available soon.
>
> Sent using BlackBerry(R) from Orange
>
> ________________________________
> From: Saad Jbabdi <[log in to unmask]>
> Date: Fri, 28 Nov 2008 18:50:43 +0000
> To: <[log in to unmask]>
> Subject: Re: [FSL] question on probability
> Hi Markus (and Yan Liu),
> I am terribly sorry, but just realised that I haven't included that fix to
> the released FSL!!! You will need to wait for the next patch now...
> And to answer your question, in principle it should underestimate waytotal
> by 50% on average if you set the option "--randfib". Otherwise it is
> difficult to predict by how much it will underestimate it for each data
> set..
> Again, I am sorry for any inconvenience.
> Cheers,
> Saad.
>
> On 28 Nov 2008, at 17:24, Markus Gschwind wrote:
>
> Dear Saad!
>
> How severe is this waytotal underestimationin in FSL 4.0.x?
> 0.1%, 10% 50%?
> Is it not possible to maybe apply a correction factor ?
> I am in the middle of a whole analysis and I have only little motivation of
> beginning again ;-)
>
> Thank you for all your work!
> Markus
>
>
>
>
>
> 2008/11/28 Saad Jbabdi <[log in to unmask]>
>>
>> Hi Yan Liu,
>> Are you using the most recent version of FSL?
>> You need FSL4.0.1 and higher, as the value in waytotal was underestimated
>> in earlier versions.
>> Cheers,
>> Saad.
>> On 28 Nov 2008, at 14:52, cathyliu wrote:
>>
>> Hi,
>>
>>
>>
>> We are doing a DTI and tractography study on the neonates with 32
>> direction DTI and b value 700. After eddy-current correction and bedpostx we
>> track the fibers using ROI positioning proposed by Mori and normalize (and
>> threshold to 5%) the results by waytotal:
>>
>>
>>
>> fslmaths fdt_paths.nii.gz –div waytotal –thr 0.05 fdt_paths_norm –odt
>> float
>>
>>
>>
>> After having analyzed 10 cases, we found that in all the cases, some of
>> the fibres we are interested in have probability more than 1, e.g. 1.5.
>>
>>
>>
>> Thanks a lot in advance for suggestions on this problem.
>>
>>
>>
>> Best Regards,
>>
>>
>>
>> Yan Liu
>> ________________________________
>> 八卦娱乐包打听,MSN资讯速递帮你忙! 了解详细!
>> ________________________________
>> 八卦娱乐包打听,MSN资讯速递帮你忙! 了解详细!
>>
>> Saad Jbabdi
>> Oxford University FMRIB Centre
>> JR Hospital, Headington, OX3 9DU, UK
>> +44 (0) 1865 222545 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
>>
>>
>>
>>
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
> 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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