In the files that you sent me earlier, the final bvecs had a set of 10 all-zero directions in the end (which I thought may have been caused by the 10 empty lines at the end of your input Tbvecs.txt) Are those zeros still there in bvecs?
On Fri, 28 Sep 2012, Loi wrote: > Hello again, > > I have tried removing the empty lines and rerunning trac-all -prep, > but the error persists. > > > Joy-Loi > > On 9/28/12, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote: >> >> There are 10 empty lines at the end of your Tbvecs.txt file. Can you try >> removing those and reruning? >> >> Hope this helps, >> a.y >> >> On Fri, 28 Sep 2012, Loi wrote: >> >>> Hello again, >>> >>> Here is the configuration file and some variations of the bvec and >>> bval files I have tried using. >>> >>> Also, I have noticed that the first time I run trac-all (without >>> specifying the bvecs and bvals), the bval file generated seems to list >>> the values twice. ie: >>> >>> 0 >>> 0 >>> 7 >>> 7 >>> 7 >>> 7 >>> 0 >>> 0 >>> 7 >>> 7 >>> 7 >>> 7 >>> >>> I hope this make sense. Thank you, >>> >>> Joy-Loi >>> >>> >>> On 9/27/12, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote: >>>> >>>> Thanks, no problem. I'd like to see the actual files on one of our >>>> machines just to make sure. >>>> >>>> On Thu, 27 Sep 2012, Loi wrote: >>>> >>>>> Hello Anastasia, >>>>> >>>>> I am in Norway and home from work for the evening, but will send you >>>>> the files first thing tomorrow morning. >>>>> Meanwhile, here is a copy of the contents in the files (as included in >>>>> my original e-mail). >>>>> Thank you for your help! >>>>> >>>>> ********************* >>>>> 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: >>>>> >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 0.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> 700.0000000 >>>>> >>>>> ********************* >>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Thu, Sep 27, 2012 at 8:14 PM, Anastasia Yendiki >>>>> <ayend...@nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> Can you please send the original bvals and bvecs files (the ones that >>>>>> you >>>>>> specify in the configuration file), and the configuration file itself? >>>>>> Thanks! >>>>>> >>>>>> a.y >>>>>> >>>>>> >>>>>> On Thu, 27 Sep 2012, Loi wrote: >>>>>> >>>>>>> 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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