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Hi! I am following your discussion with a lot of interest! Here I have a question: Why wouldn't you MULTIPLY (instead of add) the paths AB and BA? I thought it is a more conservative measure of what is in common and trancking outliers will dorp out. (And take the mean of waytotals). Thanks, Markus 2008/9/29 Matt Glasser <[log in to unmask]> > I would add the waytotals and the fdt_paths files. > > > > Peace, > > > > Matt. > > > ------------------------------ > > *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *Cherif Sahyoun > *Sent:* Monday, September 29, 2008 12:02 PM > > *To:* [log in to unmask] > *Subject:* Re: [FSL] probtrackx in MNI space > > > > Thanks Matt! > I'm pretty sure about the answer here, but just in case I'm missing some > subtlety: > I'm planning on adding the fdt-paths for tracking between 2 ROIs in each > direction to get a more reliable/complete pathway distribution. Would you > then also add the waytotals? > I'm wondering about the implications of addind vs. averaging vs. maybe > something fancier... > > 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" > Ghandi > > ------------------------------------------------------------------------------------------- > > On Sat, Sep 27, 2008 at 9:20 AM, Matt Glasser <[log in to unmask]> wrote: > > I wouldn't say that results in a given subject's DTI space are not > spatially accurate. If you want to compare your tractograghy results > directly across subjects then they will need to be in a common space like > MNI space. You can also always transform tractography results from one > space to another after the fact. I personally usually track in individual > subjects' structural spaces, as that is where I draw the ROIs, and then > transform the results into MNI space if necessary. I try to measure FA > values in native DTI space, and if I look at streamlines, I use the waytotal > output of probtrackx, rather than trying to measure anything from the path > distribution. > > > > Peace, > > > Matt. > > > ------------------------------ > > *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *Cherif Sahyoun > *Sent:* Friday, September 26, 2008 8:36 AM > > > *To:* [log in to unmask] > *Subject:* Re: [FSL] probtrackx in MNI space > > > > Thanks Matt. > So is it a fair rule of thumb to say that one should run probtrackx in MNI > space for spatially accurate results, but in DTI space for quantitative > results? > Would you ever get #streamlines or FA in MNI space? > > Thanks again, > 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" > Ghandi > > ------------------------------------------------------------------------------------------- > > On Thu, Sep 25, 2008 at 1:17 PM, Matt Glasser <[log in to unmask]> wrote: > > If you want streamlines from DTI space you should transform your ROIs from > MNI to each subject's DTI space before tractography. To measure your > subject's FA in DTI space you would do something similar. > > > > Peace, > > > > Matt. > > > ------------------------------ > > *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *Cherif Sahyoun > *Sent:* Thursday, September 25, 2008 11:49 AM > *To:* [log in to unmask] > > > *Subject:* Re: [FSL] probtrackx in MNI space > > > > Ah! I get it! So when would you ever want to track in dti space? > > > If I want to get streamline numbers/FA from a MNI space calculated tract, > is it best to transform it down to dti space and fslstats that, or to > directly get numbers from the MNI tracts in MNI space? > > ------------------------------------------------------------------------------------------ > 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" > Ghandi > > ------------------------------------------------------------------------------------------- > > On Thu, Sep 25, 2008 at 11:55 AM, Saad Jbabdi <[log in to unmask]> wrote: > > Using a mask from a higher resolution space will not give you the same > results because of interpolation. > > If you use masks in native space, the sample tracts will always start from > the centre of the voxels. If you use a higher resolution masks, the tracts > will start from different places within the native space voxels. > > > > Saad. > > > > > > On 25 Sep 2008, at 15:27, Cherif Sahyoun wrote: > > > > Thanks David and Saad! > While we're on the subject, if I'm interested in extracting number of > streamlines (and maybe FA) from paths, is running in MNI space buying me > anything but a prettier picture and the ability to get a group path? I would > think getting quantitative values is always best in native space. > Saad and I talked briefly about it, but I'm still unsure what's best if I > expect for ex. my groups to differ in the path probability but not in the > location of the path. > If I'm then looking for an average tract qualitatively, I could always just > flirt my DTI-space tracts to MNI and save myself the many extra hours, > right? > > Thanks again, > 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" > Ghandi > > ------------------------------------------------------------------------------------------- > > On Thu, Sep 25, 2008 at 6:12 AM, Markus Gschwind <[log in to unmask]> > wrote: > > Oh yes of course ;-) > Thanks, Saad! > > 2008/9/25 Saad Jbabdi <[log in to unmask]> > > > > Hi Markus, > > The resolution does not matter in the process of sampling a single > streamline (it solely depends on the step length and number of steps). > > However, the *number of voxels* of the seed mask determines the number of > sample streamlines that probtrackx will calculate. > > Since changing the image resolution changes the number of voxels in the > seed mask, resolution matters! > > > > Saad. > > > > > > On 25 Sep 2008, at 10:15, Markus Gschwind wrote: > > > > Hi! > > On the website (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_probtrackx.html) it > says: > > As explained below, results from *probtrackx* can be binned in any > available space -e.g., diffusion space, structural space or standard space. > Note, however, that tractography itself ALWAYS takes place in diffusion > space - it is simply the *results* of *probtrackx* that are stored in the > required space. > > > Thus the resolution should not make a difference...? > > Cheers, > Markus > > > > > 2008/9/24 David Gutman <[log in to unmask]> > > time is completely based on the size of your ROI, going from a > high-res to a DTI space (say your DTI was acquired at 2x2x2 and your > T1 was 1mmx1mmx1mm T1) actually is an 8 fold increase in the same > number of voxels to cover the same region-- the algorithm runs each > voxel separately, uses the supplied transformation to map it into DTI > space, and then back projects the data into whatever space you ran it > in (say hi-res T1 image). > > So basically it should take about 8 times as long depending on the > actual image dimensions your using. > > dg > > > > On Wed, Sep 24, 2008 at 10:48 AM, Cherif Sahyoun <[log in to unmask]> wrote: > > Hi, > > > > I am trying to run probtrackx in MNI space, and I've noticed that for the > same > > tracking parameters (curvature, step length, etc.) tracking in MNI takes > about > > 10hrs for given single tract vs. a couple of hours when tracking in DTI > space. > > Does that make sense? Is it just because of the higher res? > > Is this long a time generally normal? (note I am not using the -f > option). > > > > Thanks for enlightening me! > > Cherif. > > > > -- > David A Gutman, M.D. Ph.D. > Department of Psychiatry & Behavioral Sciences > Emory University School of Medicine > > > > > -- > 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 > > PS: Switzerland is a good place for scientists. It is the origin of special > relativity (1905) and the World Wide Web (1990), it is associated with 105 > Nobel laureates, and boasts the world's highest number of Nobel prizes per > capita, the highest number of publications per capita, the highest number of > patents per capita, the highest citation impact factor, the most cited > single-author paper, etc. Switzerland also got the highest ranking in the > list of happiest countries :-) . > > > > --------------------------------------------------------------------------- > > Saad Jbabdi, > > Postdoctoral Research Assistant, > > Oxford University FMRIB Centre > > > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > > +44 (0) 1865 222545 (fax 222717) > > [log in to unmask] http://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 > > PS: Switzerland is a good place for scientists. It is the origin of special > relativity (1905) and the World Wide Web (1990), it is associated with 105 > Nobel laureates, and boasts the world's highest number of Nobel prizes per > capita, the highest number of publications per capita, the highest number of > patents per capita, the highest citation impact factor, the most cited > single-author paper, etc. Switzerland also got the highest ranking in the > list of happiest countries :-) . > > > > > > --------------------------------------------------------------------------- > > Saad Jbabdi, > > Postdoctoral Research Assistant, > > Oxford University FMRIB Centre > > > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > > +44 (0) 1865 222545 (fax 222717) > > [log in to unmask] http://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 PS: Switzerland is a good place for scientists. It is the origin of special relativity (1905) and the World Wide Web (1990), it is associated with 105 Nobel laureates, and boasts the world's highest number of Nobel prizes per capita, the highest number of publications per capita, the highest number of patents per capita, the highest citation impact factor, the most cited single-author paper, etc. Switzerland also got the highest ranking in the list of happiest countries :-) .