Saad! I have still one stupid question: > 2) there is no simple answer to this, but it shouldn't matter too much > for most applications, e.g. comparing connectivity fingerprints across > subjects or across seeds. So can I run proj_thresh in a folder with subject1_seed_to_target1 subject1_seed_to_target2 subject1_seed_to_target3 subject2_seed_to_target1 subject2_seed_to_target2 subject2_seed_to_target3 all at once? I have 112 files (16 subjects) in my folder and it has been running for a while now. Does this make sence? Thanks to all your usefull explanations! Markus Quoting Saad Jbabdi <[log in to unmask]>: > > 1) the first one should work. what happens when you do that? > > 2) there is no simple answer to this, but it shouldn't matter too much > for most applications, e.g. comparing connectivity fingerprints across > subjects or across seeds. you may set the threshold to 1, which would > simply mean no thresholding at all! > > Saad. > > On 3 Jul 2008, at 12:38, Markus Gschwind wrote: > >> Thank you Saad! >> >> So I tried - but >> >> 1.) it seems that I am struggeling with the "list_of_volumes": >> >> I have them all in one folder like: >> subject1_seed1_2_target1 >> subject1_seed1_2_target2 >> subject1_seed1_2_target3 >> subject1_seed1_2_target4 >> >> I tried the command >> proj_thresh thisfolder/* threshold >> >> no success, >> >> neither with a list which I entered into a txt-file (cannot read this file) >> proj_thresh .../listofvolumes.txt threshold >> >> How do I have to feed in this list of volumes? >> >> 2.) How do I determine the threshold? >> >> Thanks! >> Markus >> >> >> >> Quoting Saad Jbabdi <[log in to unmask]>: >> >>> 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 >>> --------------------------------------------------------------------- --- >>> --- >> >> >> >> -- >> >> 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