On Mon, Dec 1, 2008 at 5:41 PM, Matt Glasser <
[log in to unmask]> wrote:
> I don't think using the max value of the fdt_paths is a good idea. That
> will vary depending on how closely packed the samples are at the narrowest
> point of the tract. For example if you have a 100000 sample pathway that at
> its narrowest point goes through a single voxel, that voxel's value would be
> 100000, and that would be the max of the fdt_paths. If you had a separate
> 100000 sample pathway that at its narrowest point was divided evenly among 4
> voxels, the maximum value of the fdt_paths would be 25000. Normalizing
> based on this number would give you very different probability values across
> the entire pathway, even if the two were otherwise identical.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:
[log in to unmask]] On Behalf
> Of Cherif Sahyoun
> Sent: Monday, December 01, 2008 4:10 PM
> To:
[log in to unmask]
> Subject: Re: [FSL] question on old and new waytotals
>
> Hi Saad,
>
> Can you talk about the implications of using something other than the
> waytotal for normalizing? I'll get you started :)
>
> - using waytotal would give the conditional probability of going
> through a given voxel, given that there is a path.
> - using the ROI_size*samples would give the absolute probability of
> going through a voxel (on the path)
> What to you think of using the max value of the fdt_paths? That should
> give a normalized conditional probability similar to using waytotal
> (though obviously we important differences since now we are forcing
> the most likely voxels to have a probability of 1, which was not the
> case using waytotal)...
> If what one wants is just to normalize across subjects to be able to
> compare mean p of a tract, I guess that would work?
>
> Best,
> Cherif
>
> ----------------------------------------------------------------------------
> --------------
> 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"
> Gandhi
> ----------------------------------------------------------------------------
> ---------------
>
>
>
> On Mon, Dec 1, 2008 at 4:54 PM, Saad Jbabdi <
[log in to unmask]> wrote:
>> Hi Markus,
>> When you say 50 papers, you must be thinking of the seed_to_target values,
>> not waytotal, am I right? The output of seed_to_target is NOT
>> underestimated, it is only waytotal.
>> the waytotal file is a recent output in probtrackx, so I would be
> surprised
>> if there were 50 articles published that are using it!
>> To answer your question, I think it is quite hard to predict the behaviour
>> of waytotal as it is now, so I would recommend re-running your analysis
> with
>> the patch to come if you are planning to use waytotal.
>> Cheers,
>> Saad.
>>
>> On 1 Dec 2008, at 17:20, Markus Gschwind wrote:
>>
>> That is very good news! Thank you so much!
>>
>> However, I am really curious if there is an officially recommended way of
>> dealing with this underestimation. Roughly guessed, there are about 50
>> publications using those "old" waytotals and if I contribute another one,
>> now that it is known that those values are not always true...
>> Should all the people who are still working with FSL 4.0.x really restart
>> the whole analyis in FSL 4.1?
>>
>> Would there be another way?
>>
>> Many regards,
>> Markus
>>
>>
>>
>>
>>
>> 2008/12/1 Saad Jbabdi <
[log in to unmask]>
>>>
>>> Hi All,
>>>
>>> The patch -should be- available tomorrow :-)
>>>
>>> Thank you all for pointing this out!
>>>
>>> Cheers,
>>> Saad.
>>>
>>>
>>> On 28 Nov 2008, at 20:23, Martin Kavec wrote:
>>>
>>>> Thanks a lot Saad,
>>>>
>>>> at least we helped to point out the problem. Could you please let us
>>>> know,
>>>> when we could expect the patch?
>>>>
>>>> Thanks,
>>>>
>>>> Martin
>>>>
>>>> On Friday 28 November 2008 19:50:43 Saad Jbabdi wrote:
>>>>>
>>>>> 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.
>>>>
>>>>
>>>> --
>>>> **********************************
>>>> Senior Clinical Research Associate
>>>> MRI Unit of the Department of Radiology
>>>> Erasme Hospital
>>>> Lennik Street 808
>>>> B-1070 Brussels
>>>> BELGIUM
>>>>
>>>> tel: +32-2-555-4325
>>>> fax: +32-2-555-3994
>>>> email:
[log in to unmask] >>>> **********************************
>>>>
>>>> -----------------------------------------------
>>>> Find a way, or make one!
>>>>
>>>
>>> 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 >>
>>
>>
>>
>>
>>
>
