This is a great point and while I have been using path distributions,
I'd like to compare my results to using the seeds_to_targets outputs.
I realize that a seed voxel may track through it's neighbors and
increase their value, but if a group of voxels is consistently
included in a track to the target (even if these streamlines
"originated" in other seed voxels), it may be that these are of
importance. This is why I normalize to an individual and then compare
this spatial distribution of importance across a group. If it happens
that I did not do a good job of segmenting out the white matter, then
the voxels with the highest values will be in regions with high
partial volumes of WM. But what I have been finding is that there are
hotspots in a group-level seed mask when tracking to a target with
known anatomical connectivity, but if you move this target to an
adjacent region you can actually disrupt the pattern and lose sign of
any hotspots. I'm still working through more negative controls like
this and can let people know what I find if there is any interest.
As for the application, I am comparing controls to a group of
patients that I believe have an abnormality in the formation of a
specific tract. So far, the analysis fits the hypothesis (knock on
wood). Also, we have a few projects looking at things like somatotopy
and it would be interesting to see if there are any anatomical
correlates that match up with the functional findings.
Thanks for the comments,
ted
On Dec 6, 2008, at 12:20 PM, Matt Glasser wrote:
> Are you doing this with seeds to targets output or the path
> distribution
> output? I can see the possibility of some samples from one seed
> ending up
> in another seed and artificially increasing its value. With the
> seeds to
> targets output you can be sure there is no such double counting
> (and can
> still use this output to normalize the path distribution).
>
> This is an interesting approach. I am curious what questions, in
> general,
> you are trying to ask with it.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Ted Yanagihara
> Sent: Friday, December 05, 2008 12:05 AM
> To: [log in to unmask]
> Subject: Re: [FSL] question on old and new waytotals
>
> This has been a great discussion and it will be interesting to see
> how tractography analysis techniques evolve in the future.
>
> We have been testing the reproducibility of one method that is
> similar to the earlier idea of normalizing to the maximum paths,
> which has flaws as Matt has pointed out, and I was hoping to get some
> feedback from the list. Our approach is aimed at making a qualitative
> comparison of voxels within the seed mask to test hypotheses across a
> group and between groups. We start by performing seed->waypoints/
> termination tractography, then extracting all the streamline values
> in the seed mask, without any thresholding applied to the image, then
> normalize to the maximum value in the seed. This gives us the
> relative "importance" of a seed voxel in connecting to the target. We
> can then add these images across the group and again normalize to the
> maximum. Our group result then illustrates foci of important voxels
> within the seed on the group level. What we would now like to do is
> perform a simple ttest or regression for hypothesis-testing. Have
> others tried similar approaches and have any suggestions?
>
> I'll also add that we too have tried multiple ways of establishing a
> set of metrics by which to standardize tractography results across
> subjects with little luck.
>
> Any comments would be appreciated.
>
> ted
>
>
> On Dec 4, 2008, at 10:07 PM, Matt Glasser wrote:
>
>> My understanding is that dividing by the waytotal is the way to
>> normalize
>> across subjects as best as you can. Then you could threshold at some
>> fractional proportion of the waytotal and binarize. This should
>> give you
>> the most similar spatial distributions across subjects. However, I
>> think
>> that this method is less useful when you are making comparisons
>> within a
>> brain, for example between the same pathway in the two hemispheres,
>> when you
>> are interested in pathway asymmetries for example.
>>
>> Peace,
>>
>> Matt.
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf
>> Of David Gutman
>> Sent: Thursday, December 04, 2008 8:46 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] question on old and new waytotals
>>
>> I'v talked with Matt about this issue in the past. Other than
>> controlling for the volum of the seed you use (which since I run most
>> things in a standard space isn't an issu) just dividing by the
>> total #
>> of threads, which should be the same across subjects, would just
>> scale
>> the images, but not actually "normalize" between subjects.
>>
>> Generally it seems the "trackability" really does significantly vary
>> between subjects. The variance between subjects is very unlikely due
>> to some real biological difference, since the variance is sometimes
>> on the order of 1-2 magnitudes between subjects, in terms of the
>> "raw"
>> number of fibers that may make it from seedmask A to targets B and C.
>> I'll see numbers vary from the 100's in subject 1 to the thousands or
>> even 10s of thousands between subjects....
>>
>>
>> Ive played around in the past, as I said, with some internal standard
>> "non" interesting tract but was never super happy with the results.
>> Maybe Tim/Saad/Steve or some of the more physics minded people have
>> some thoughts about this-- in particular maybe looking at the
>> variance
>> in one of the FA derived metrics (and I won't pretend to fathom which
>> one) that could be used as some sort of pseudo-objective standard of
>> DTI image quality across some large/homogenous region of cortex (if
>> such a thing exists....)
>>
>>
>> DG
>>
>>
>>
>> On Thu, Dec 4, 2008 at 8:42 PM, Cherif Sahyoun <[log in to unmask]>
>> wrote:
>>> Hi David,
>>>
>>> I like the internal standard idea. As you pointed it is hard to
>>> implement/justify though.
>>> Perhaps something based on the eigenvalues could be used to quantify
>>> Oo the "trackability" of each subject...
>>>
>>> The percentage idea is basically what I had in mind when talking
>>> about
>>> dividing by the max (or 98th percentile), but see also Matt's
>>> concerns.
>>>
>>> Thanks,
>>> Cherif
>>>
>>>
>>> On Thu, Dec 4, 2008 at 8:08 PM, David Gutman <[log in to unmask]>
>>> wrote:
>>>> Cherif I have noted similar absolute number differences between
>>>> subjects, like a scaling difference, where the tracts themselves
>>>> look
>>>> extremely similar. My current thoughts are that the
>>>> "trackability" of
>>>> an image varies significantly from subject to subject depending on
>>>> things like you mentioned, scan quality, motion, etc...
>>>>
>>>>
>>>> One thing I was thinking of, almost analogous to other
>>>> methodologies
>>>> (like when you try and amplify DNA/RNA you may choose a gene that
>>>> "shouldn't be different" to serve as a loading control and use
>>>> that to
>>>> scale all of your values... myosin or actin or other messenger
>>>> genes
>>>> are often used in this sort of analysis, and the relative
>>>> mRNA/whatever expression is correlated using some sort of internal
>>>> standard....
>>>>
>>>> For DTI, I am unaware of any "internal standard"/tract that
>>>> could be
>>>> used for comparison, and have played around with this in the past
>>>> (although it's been a while). I'd really like to get other
>>>> people's
>>>> feedback on this concept; in particular it would be nice to pick a
>>>> relatively uninteresting region (or combination of regions) where
>>>> you
>>>> say calculate the number of fibers along the optic radiations, or
>>>> maybe part of the corpus collosum and for every subject tract the
>>>> number of fibers that make it from A to B and then use this
>>>> reference
>>>> tract to scale all of your more "interesting" tracts.... so
>>>> basically
>>>> pick a region that you think should not change between
>>>> people/subjects/whatever...
>>>>
>>>> Also just looking at relative percentages instead of absolute
>>>> numbers
>>>> may get around this sort of issue of just looking at raw numbers
>>>> which
>>>> is often what I wind up doing (although this also can have its
>>>> pitfalls).
>>>>
>>>>
>>>> DG
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> It's been an issue I've been thinking about for quite some time,
>>>> but I
>>>>
>>>> On Thu, Dec 4, 2008 at 7:49 PM, Cherif Sahyoun <[log in to unmask]>
>>>> wrote:
>>>>> 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 <matt@ma-
>>>>>>>>>>> tea.com>
>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> David A Gutman, M.D. Ph.D.
>>>> Department of Psychiatry & Behavioral Sciences
>>>> Emory University School of Medicine
>>>>
>>>
>>
>>
>>
>> --
>> David A Gutman, M.D. Ph.D.
>> Department of Psychiatry & Behavioral Sciences
>> Emory University School of Medicine
>>
>
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