Oh of course! Sorry, I should not email at 2 AM, uncaffeinated!
The reason I wanted to use something based on the pathway itself is
because of the wide variability in numbers between subjects. There are
different ranges of values between subjects, which cannot be explained
by the size of the ROI, making comparison difficult. This may be due
to the quality of the scans, slightly more motion, etc. but the tracts
still look great, so I really think they are normal subject-specific
variance and not a "problem" per se.
With that in mind, waytotal normalization made most sense to me, but
now I'm a bit stuck with many tracts already run, hence the new
suggestions...
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 Thu, Dec 4, 2008 at 9:52 AM, Matt Glasser <[log in to unmask]> wrote:
> You could also normalize/threshold according to the total number of samples
> sent out (# voxels in seed ROIs X # of samples sent out from each voxel). I
> don't think you want to normalize based on something that is dependant on
> the spatial distribution of the pathway, which the 98th percentile will
> still be.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Cherif Sahyoun
> Sent: Thursday, December 04, 2008 12:55 AM
> To: [log in to unmask]
> Subject: Re: [FSL] question on old and new waytotals
>
> Hey Matt,
>
> Thanks for the quick reply. What do you mean by "two" good options?
> the first is re-running probtrackx and getting waytotal out. What's
> the second?
> I thought the 98th percentile might get around (to some extent) the
> max issue, since we're less sensitive to the size of the core.
>
> 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 9:41 PM, Matt Glasser <[log in to unmask]> wrote:
>> I don't think that is a good idea for the same reason I stated for the
> max.
>> Now that the waytotal bug has been fixed, you have two good options. The
>> waytotal measures more accurately what you are trying to get at via using
>> the max or the 98th percentile.
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
>> Of Cherif Sahyoun
>> Sent: Wednesday, December 03, 2008 6:37 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] question on old and new waytotals
>>
>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
|
