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