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Dear Elin, You seem to be right - bugger!! Thanks for finding that. I'll email about patches shortly. Tim On Wed, 25 May 2005, Elin Lundström wrote: > Hello, > > I am using FSL with the Linux Mandrake operative > system. Earlier I had problems with FLIRT so Mark > Jenkinson made a new version of FLIRT which I > downloaded. Now when I run FEEDS (with my new fsl > version), I get some errors. I put the run output at > the end of this mail and the result directory at > http://www.smile.ki.se/results.tar.gz. I have run > eddycorrect on several brains and I am a bit worried > that the FLIRT error will have affected the results. > > I also have another problem: I have calculated FA and > MD values on a couple of pixels manually, starting > from eddy current corrected brains. Unfortunately I > did not get the same values as DTIFit. I have looked > at the dtifit.cc to see the formulae you are using. I > saw one formula saying: > > float numer=(1.5*(Dd(1)-mDd)*(Dd(1)-mDd)... and so on > > If I am not mistaken it seems like there is a > parenthesis missing (in order to multiply all > eigenvalues with 1.5). Could you please give me the > exact formulae that you have used to calculate MD and > FA so that I can compare it with my manually > calculated ones? > > Thank you for your time! > > Best regards, > Elin > > > > [elin@freja feeds]$ time ./RUN all > > FSL Evaluation and Example Data Suite v3.2 > > start time = Wed May 25 13:45:37 CEST 2005 > hostname = freja.hs.sll.se > os = Linux freja.hs.sll.se 2.4.25eva_patch #1 SMP Mon > Apr 5 16:52:08 CEST 2004 i686 unknown unknown > GNU/Linux > > > /bin/rm -rf /home/elin/test_fsl/feeds/results ; mkdir > /home/elin/test_fsl/feeds/results > > > Starting PRELUDE & FUGUE at Wed May 25 13:45:37 CEST > 2005 > % error = 0.0 > % error = 0.0 > > Starting SUSAN at Wed May 25 13:45:41 CEST 2005 > % error = 0.0 > > Starting SIENAX (including testing BET and FLIRT and > FAST) at Wed May 25 13:47:39 CEST 2005 > checking error on BET: > % error = 0.0 > checking error on FLIRT: > % error = 1085.46 > Warning - test failed! > checking error on FAST: > checking error on single-image binary segmentation: > % error = 2.07 > Warning - test failed! > checking error on partial volume images: > % error = 1.1 > Warning - test failed! > % error = 0.44 > % error = 0.28 > checking error on SIENAX volume outputs: > % error = 0.17 > % error = 0.02 > % error = 0.57 > % error = 0.46 > % error = 1.03 > Warning - test failed! > > Starting BET2 at Wed May 25 14:03:19 CEST 2005 > checking error on T1 brain extraction: > % error = 0.0 > checking error on skull and scalp surfaces: > % error = 0.09 > % error = 0.16 > % error = 0.32 > > Starting FEAT at Wed May 25 14:30:59 CEST 2005 > checking error on filtered functional data: > % error = 0.19 > checking error on raw Z stat images: > % error = 0.33 > % error = 0.17 > % error = 0.3 > checking error on thresholded Z stat images: > % error = 0.29 > % error = 0.18 > % error = 0.35 > checking error on position of largest cluster of > Talairached zfstat1: > % error = 0.0 > % error = 0.0 > % error = 0.1 > % error = 0.07 > % error = 0.1 > % error = 0.19 > > Starting MELODIC at Wed May 25 14:49:36 CEST 2005 > % error = 0.0 > > Starting FDT (bedpost) at Wed May 25 15:09:08 CEST > 2005 > checking error on bedpost output: > % error = 0.25 > % error = 0.02 > % error = 0.07 > % error = 0.07 > % error = 0.1 > % error = 0.22 > % error = 0.22 > > Warning - not all tests passed > > end time = Wed May 25 15:50:14 CEST 2005 > > 6818.41user 269.82system 2:04:37elapsed 94%CPU > (0avgtext+0avgdata 0maxresident)k > 0inputs+0outputs (645543major+28231604minor)pagefaults > 0swaps > [4]+ Done emacs dtifit.cc (wd: > ~/fsl/src/fdt) > (wd now: ~/test_fsl/feeds) > [elin@freja feeds]$ > -- ------------------------------------------------------------------------------- Tim Behrens Centre for Functional MRI of the Brain The John Radcliffe Hospital Headley Way Oxford OX3 9DU Oxford University Work 01865 222782 Mobile 07980 884537 -------------------------------------------------------------------------------