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 > > > _______________________________________________ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
