Hey Saad, Matt, and the Gang,
Does anyone has thoughts on using the upper output of fslstats -r as a
normalizing factor?
Thanks,
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 Wed, Dec 3, 2008 at 1:47 PM, Saad Jbabdi <[log in to unmask]> wrote:
> No, waytotal is independent of seed_to_target.
> maybe the confusion comes from the fact that your are talking about
> seed_to_target, but what you mean is setting waypoints and exclusion masks.
> seed_to_target (at least for us) refers to the classification targets (as
> the output of such analysis are called seed_to_<target>).
> so here is a summary of what happens (hopefully to avoid confusion, rather
> than add to it!);
> . waytotal counts the number of non-rejected tracts.
> . if waypoint masks or exclusion masks are used, then waytotal should go
> down (or eventually doesn't change)
> . if waypoint masks or exclusion masks are NOT used, then waytotal should be
> equal to the total number of requested samples (i.e. no sample has been
> rejected)
> . setting classification targets (seed_to_target) does NOT affect waytotal.
> . the values calculated in seed_to_target are not affected by the recent
> patch (FSL4.1.2), since their values were NOT underestimated.
> I hope this was clear?
> Cheers,
> Saad.
>
> On 3 Dec 2008, at 18:12, Markus Gschwind wrote:
>
> Saad,
> just one other thing:
>
> It is only the Seed_to_target-waytotal which is wrong, not the seed
> (alone)-waytotal, right?
>
> Thanks, Markus
>
>
> 2008/12/3 Markus Gschwind <[log in to unmask]>
>>
>> Hi Saad!
>> That is fantastic news!
>> I am curious if it changes my waytotals!
>> Thanks for your high presence here in the list!
>> Markus
>>
>>
>> 2008/12/3 Saad Jbabdi <[log in to unmask]>
>>>
>>>
>>> Hello Saad!
>>>
>>>> ...so I would be surprised if there were 50 articles published that are
>>>> using it!
>>>
>>> Sorry. I was just guessing out of my guts... I overestimated the
>>> importance of probtrackx ;-)
>>>
>>> I was actually referring to waytotal. I'm sure there are many papers
>>> using probtrack(x) :-)
>>>
>>>
>>> Can the patch also be installed to FSL 4.0.4?
>>>
>>> You can use the probtrackx binary (copy it into $FSLDIR/bin), but you
>>> can't mix the source files if you need your own build...
>>>
>>> Cheers,
>>> Saad.
>>>
>>>
>>>
>>> Thank you for your support!
>>> Markus
>>>
>>>
>>> 2008/12/1 Cherif Sahyoun <[log in to unmask]>
>>>>
>>>> I see, so this will be too dependent on how much overlap there is at the
>>>> core...
>>>> Any other possibilities? maybe using a percentile? (upper output of
>>>> fslstats -r)?
>>>>
>>>>
>>>> ------------------------------------------------------------------------------------------
>>>> 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 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
>>>> >>
>>>> >>
>>>> >>
>>>> >>
>>>> >>
>>>> >>
>>>> >
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>> --
>> 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
>
>
>
> --
> 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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