[Freesurfer] TRACULA error "R: Subscript out of range"

Hi all,

I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is exiting with the output below. Most notably, I think, is the section of the output that says "R: Subscript out of range.” repeatedly and then the section afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8 9 / ERROR: valid frame numbers are between 0 and 0”. Does anyone have thoughts on what might be going on here?

I’ve attached my bvecs and bvals too, in case there is trouble there too.

Thanks very much for any help.

Best, Anna

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INFO: SUBJECTS_DIR is /mindhive/nklab/u/amynick/Tracula/Tracula_trio/diffusion_recons INFO: Diffusion root is /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial Actual FREESURFER_HOME /cm/shared/openmind/freesurfer/6.0.0 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cm/shared/openmind/freesurfer/6.0.0 Previous: /software/pkg/freesurfer/freesurfer-6.0.0 trac-preproc -c /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/dmrirc.local -log /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/trac-all.log -cmd /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/trac-all.cmd #------------------------------------- /cm/shared/openmind/freesurfer/6.0.0/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Nov 30 13:40:35 EST 2017 mri_convert --bvec-voxel /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm... Getting Series No INFO: Found 4505 files in /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig INFO: Scanning for Series Number 1 Scanning Directory INFO: found 128 files in series INFO: loading series header info.

RunNo = 0 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 INFO: (160 160 128), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;

FileName /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName KanCon02 Date and time StudyDate 20161216 StudyTime 163713.171000 SeriesTime 164740.250000 AcqTime 164708.722500 Acquisition parameters PulseSeq *fl3d1_ns Protocol AAHScout_32ch PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 1.37 InversionTime -1 RepetitionTime 3.15 PhEncFOV 260 ReadoutFOV 260 Image information RunNo 0 SeriesNo 1 ImageNo 1 NImageRows 160 NImageCols 160 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 101.6000 130.0000 130.0000 VolRes 1.6250 1.6250 1.6000 VolDim 160 160 128 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -0.8000 0.0000 0.0000 TransferSyntaxUID unknown UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=3.15, TE=1.37, TI=-1.00, flip angle=8.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz... mri_probedicom --i /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm > /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dcminfo.dat cp /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/gradients.txt /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs cp /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/bvalues.txt /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.tmp /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvals.tmp /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals orientLAS /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz INFO: input image orientation is PIL INFO: input image determinant is -4.225 mri_convert -oni 128 -onj 160 -onk 160 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -0.812503 1.625 1.6125 -rt nearest /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 160 -onk 160 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -0.812503 1.625 1.6125 -rt nearest /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz... TR=3.15, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Reslicing using nearest writing to /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz... INFO: found /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals, copying INFO: found /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs, converting to LAS mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.bvecs /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.bvals /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvals eddy_correct /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz 0 processing /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_tmp0000 mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.norot xfmrot /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.ecclog /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.norot /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs R: Subscript out of range. 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R: Subscript out of range. ln -sf /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/data.nii.gz mri_convert --frame 0 1 2 3 4 5 6 7 8 9 /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/lowb.nii.gz mri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9 /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frames 0 1 2 3 4 5 6 7 8 9 ERROR: valid frame numbers are between 0 and 0 Linux node044 3.10.0-514.26.2.el7.x86_64 #1 SMP Tue Jul 4 15:04:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Thu Nov 30 13:44:15 EST 2017