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Hi Markus, It shouldn't matter which way you do it, but you don't want to do separate calls to probtrackx for that, since it is much faster to do it all in once! Saad. On 3 Jul 2008, at 08:52, Markus Gschwind wrote: > Thanks a lot Saad! > > Now it is clearer. > > Just in order to understand it better: > > Is it thus only possible to used proj_thresh if I have > "probtrackxed" with MORE THAN ONE classification targets in ONE > command > probtrackx seed1 to target1 /target2 / target3 -os2t > > or can I also take several seed_to_blahs together from several > probtrackx runs from the same seedmask > probtrackx seed1 to target1 -os2t > probtrackx seed1 to target2 -os2t > probtrackx seed1 to target3 -os2t > > and then run proj_thresh on them? > > Thanks again! > Markus > > > Quoting Saad Jbabdi <[log in to unmask]>: > >> Hi Markus, >> >> proj_thresh is suitable as a within-subject tool. I don't think it >> does make sense to use it as a between-subject tool as you have >> suggested. It is however meant to give (within-subject) results that >> are more comparable between subjects! >> >> proj_thresh does the following: >> say you have a seed voxel for which you ran probtrackx with 3 >> "classification targets" A, B and C. >> Then probtrackx will give you three files called seed_to_<A,B,C>. >> Say now that for this particular seed voxel, the values in >> seed_to_blah are: >> seed_to_A: 10 >> seed_to_B: 100 >> seed_to_C: 150 >> (these numbers do not necessarily sum to the total number of samples >> ran from the seed voxel, since some of the sample tracts might not >> connect to either A,B or C). >> >> Then if you run proj_thresh with a threshold of 10 or less, you >> will have: >> seed_to_A_proj_seg_thr: 10/(10+100+150) = 0.0385 >> seed_to_B_proj_seg_thr: 100/(10+100+150) = 0.385 >> seed_to_C_proj_seg_thr: 150/(10+100+150) = 0.5769 >> >> If you choose a threshold of 11 (or more and <=100): >> seed_to_A_proj_seg_thr: 0/(0+100+150) = 0 >> seed_to_B_proj_seg_thr: 100/(0+100+150) = 0.4 >> seed_to_C_proj_seg_thr: 150/(0+100+150) = 0.6 >> >> >> I hope this makes it a bit clearer? >> Saad. >> >> >> >> On 2 Jul 2008, at 16:16, Markus Gschwind wrote: >> >>> Hello FSL experts! >>> >>> I have a question concerning the *proj_thresh* function. >>> >>> There is not so much on the site and neither in the forum. >>> >>> Is correct to use it as a within-subject tool in order to >>> evaluate the seeds going from a given seedmask to differnt >>> target masks >>> list of volumes : >>> subject1_seed1_2_target1 >>> subject1_seed1_2_target2 >>> subject1_seed1_2_target3 >>> subject1_seed1_2_target4 >>> etc >>> >>> or is it a between-subject tool to evaluate the seeds coming >>> from the same seedmask and going to the same targe mask? >>> subject1_seed1_2_target1 >>> subject2_seed1_2_target1 >>> subject3_seed1_2_target1 >>> subject4_seed1_2_target1 >>> etc. >>> >>> On the website it says: >>> For each voxel in the seeds mask that has a value above threshold >>> *[which I have do define, e.g. if I have 20 subjects I take 20. >>> Correct?]* for at least one target mask, proj_thresh calculates >>> the number of samples reaching each target mask as a proportion >>> of the total number of samples reaching any target mask. The >>> output of proj_thresh is a single volume for each target mask. >>> >>> What disturbed me was that I got for each subject[xy] >>> _seed1_2_target1 a volume s[xy] >>> _myseed_seed_proj_seg_thr_14.nii.gz and each one looks >>> different... >>> >>> I seem not to understand this function. >>> >>> Could anyone explain a little bit please? >>> >>> Thanks a lot!! >>> Markus >>> >>> >>> -- >>> >>> 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, >> 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 >> --------------------------------------------------------------------- >> --- --- > > > > -- > > 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, 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 ------------------------------------------------------------------------ ---