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
>>
>>
>>
>>
>>
>>
>
|