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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> > > --------------------------------------------------------------------------- > > > > > > > > > > > > >