Hello, I generate the files in Linux (using gedit) and they look normal (I have compared them to the files in the tutorial).
So far I have tried ending both with and without .txt, transposing the files, changing to equal number of decimals and adding 'setenv LC_ALL en_US' to the .tchsrc file. The inputs I am using are dicoms, and even though I specify a path to the b-value files and gradient tables I make (I originally didn't specify these, and got the same error message), new bvecs and bvals are generated in the trac-all -prep process, leading to the error. Thank you, Joy-Loi On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Joy - How were your bvecs and bvals files generated? In the past some > people have had problems with files exported from Excel b/c it generates > text files with Windows-specific end-of-line characters that cannot be read > properly on Linux. Do the files look normal when you run "more" on them on > the system where you ran trac-all? > > a.y > > > On Wed, 26 Sep 2012, Loi wrote: > >> Dear FreeSurfers, >> >> I am trying to run trac-all -prep on a single subject, and get the >> following error: >> >> dtifit -k >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz >> -m >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz >> -r >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs >> -b >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals >> -o >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit >> Error: bvecs and bvals don't have the same number of entries >> >> I have searched the message thread, and cannot seem to find a solution >> applicable to my situation: it seems that the trac-all process >> generates transposed bvec and bval files. >> Therefore, I tried transposing these manually and specifying the >> location to these files (as explained in the tutorial: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but >> attempting to run trac-all again still leads to the same result: new >> bval and bvec files are generated, and I receive the same error >> message. >> >> Does anyone know how I can solve this problem? >> >> Thank you, >> Joy-Loi >> >> >> ********************* >> My configuration file: >> >> >> setenv SUBJECTS_DIR >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons >> >> set dtroot = >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >> >> set subjlist = id101 >> set runlist = 1 >> >> set dcmroot = >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >> set dcmlist = id101/orig/1.dcm >> >> set bvalfile = >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt >> >> set bvecfile = >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt >> >> set nb0 = 10 >> >> set doeddy = 1 >> set dorotbvecs = 1 >> set thrbet = 0.3 >> set doregflt = 1 >> set doregbbr = 0 >> set doregmni = 1 >> set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz >> >> #set trainfile = >> >> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt >> >> set pathlist = (lh.cst_AS rh.cst_AS \ >> lh.ilf_AS rh.ilf_AS \ >> lh.unc_AS rh.unc_AS \ >> fmajor_PP fminor_PP \ >> lh.atr_PP rh.atr_PP \ >> lh.cab_PP rh.cab_PP \ >> lh.ccg_PP rh.ccg_PP \ >> lh.slfp_PP rh.slfp_PP \ >> lh.slft_PP rh.slft_PP) >> >> >> set ncpts = 5 >> >> set usetrunc = 1 >> >> >> >> >> >> ********************* >> My bvals: >> >> 0.000000 >> 0.000000 >> 0.000000 >> 0.000000 >> 0.000000 >> 0.000000 >> 0.000000 >> 0.000000 >> 0.000000 >> 0.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> 700.000000 >> >> ********************* >> My bvecs: >> >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> 0.0000000 0.0000000 0.0000000 >> -0.9998760 0.0011040 0.0157340 >> -0.7705615 0.6320276 0.0823114 >> -0.2461791 0.0273479 0.9688392 >> -0.7953558 0.1076421 0.5965091 >> 0.4620816 -0.8755928 0.1407778 >> 0.2261090 -0.8553081 -0.4661796 >> 0.2601186 0.4095102 -0.8744363 >> -0.7969547 -0.5877791 0.1392076 >> -0.5028073 -0.5104712 0.6975709 >> -0.3073035 0.1334521 -0.9422074 >> 0.7957742 0.1950272 -0.5733304 >> 0.8041493 0.5924478 -0.0484727 >> -0.1867079 -0.9528833 0.2390659 >> 0.3898569 -0.1063898 0.9147088 >> 0.1341999 -0.6614532 0.7378819 >> 0.3382555 0.8823941 0.3270553 >> -0.7688307 -0.3139264 -0.5570900 >> -0.4086013 0.6653325 0.6248017 >> -0.2933309 0.7581020 -0.5824408 >> 0.7689370 -0.4282441 0.4747016 >> 0.1800972 0.5296402 0.8288835 >> 0.7680658 0.3158178 0.5570763 >> -0.2214999 0.9744585 0.0370050 >> -0.4175692 -0.8418782 -0.3418731 >> -0.1784475 -0.4817282 -0.8579599 >> 0.3361637 0.8554551 -0.3939400 >> 0.7858656 -0.5091907 -0.3509137 >> 0.4194232 -0.2589429 -0.8700761 >> -0.7760561 0.3511497 -0.5238622 >> 0.9987836 -0.0413076 0.0269219 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. 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