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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 <http://www.fmrib.ox.ac.uk/%7Esaad> >> >> >> >> >> >> >> >> -- >> >> 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 <http://www.fmrib.ox.ac.uk/%7Esaad> >> >> >> >> >> >> >> >> >> >> >> >> >> > >> > > > > -- > 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 <http://www.fmrib.ox.ac.uk/%7Esaad> > > > > > > > -- 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