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.

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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)









--
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)