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I have been attempting to run TRACULA on the sample practice data using the sample configuration file listed here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula. I am using Free Surfer 6. I receive an error message at the first step of the pre-processing pathway with subjects elmo.2008 and elmo.2012. It looks like it may be getting hung up at the Eddy Correction step. Do you know why this might be happening? Thank you for your help! Jason *This is the configuration file:* # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = $TUTORIAL_DATA/diffusion_tutorial # Subject IDs # set subjlist = ( elmo.2005 \ elmo.2008 \ elmo.2012 ) # Input diffusion DICOMs # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) # set dcmroot = $TUTORIAL_DATA/diffusion_tutorial set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \ elmo.2008/orig/97000-000017-000001.dcm \ elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 ) # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bveclist = ( $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/orig/gradients.txt \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2008/orig/gradients.txt \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/orig/gradients.txt ) #set bvecfile = /path/to/bvecs.txt # Diffusion b-value tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvallist = ( $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/orig/bvalues.txt \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2008/orig/bvalues.txt \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/orig/bvalues.txt ) #set bvalfile = /path/to/bvals.txt set runlist = (2) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 set doregmni = 1 set doregcvs = 0 #set mnitemp = /path/to/mni/template #set cvstemp = /cvs/template/name #set cvstempdir = /path/to/parent/dir/of/cvstemp set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) *This is the attempted run:* [jar269@librapet ~]$ trac-all -corr -c /home1/jar269/Elmo2/dmrirc.tutorial INFO: SUBJECTS_DIR is /home1/jar269/Elmo2/diffusion_recons INFO: Diffusion root is /home1/jar269/Elmo2/diffusion_tutorial Actual FREESURFER_HOME /home1/am2359/freesurfer_6 trac-preproc -c /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/dmrirc.local -log /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/trac-all.log -cmd /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/trac-all.cmd #------------------------------------- /home1/am2359/freesurfer_6/bin/trac-preproc #------------------------------------- #@# Image corrections Sun Jul 12 14:27:04 EDT 2020 mri_convert --bvec-voxel /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm... Getting Series No INFO: Found 74 files in /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig INFO: Scanning for Series Number 17 Scanning Directory INFO: found 70 files in series INFO: loading series header info. RunNo = 16 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName CON04_07172008 Date and time StudyDate 20080717 StudyTime 082602.097000 SeriesTime 091538.382000 AcqTime 091309.512500 Acquisition parameters PulseSeq ep_b0#1 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 9850 PhEncFOV 237 ReadoutFOV 237 Image information RunNo 16 SeriesNo 17 ImageNo 1 NImageRows 1152 NImageCols 1152 NFrames 70 SliceArraylSize 79 IsMosaic 1 ImgPos 1042.7820 1078.5270 242.5410 VolRes 1.8516 1.8516 1.8500 VolDim 128 128 79 Vc -0.9997 -0.0232 -0.0095 Vr 0.0249 -0.9576 -0.2870 Vs -0.0024 -0.2872 0.9579 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 79), nframes = 70, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9850, TR = 9850 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.99969 -0.02379 0.00778 -0.14012; 0.02316 0.99706 0.07309 -9.34992; -0.00949 -0.07288 0.99730 -12.79552; 0.00000 0.00000 0.00000 1.00000; FileName /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName CON04_07172008 Date and time StudyDate 20080717 StudyTime 082602.097000 SeriesTime 091538.382000 AcqTime 091309.512500 Acquisition parameters PulseSeq ep_b0#1 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 9850 PhEncFOV 237 ReadoutFOV 237 Image information RunNo 16 SeriesNo 17 ImageNo 1 NImageRows 1152 NImageCols 1152 NFrames 70 SliceArraylSize 79 IsMosaic 1 ImgPos 118.6930 148.7646 -38.5453 VolRes 1.8516 1.8516 1.8500 VolDim 128 128 79 Vc -0.9997 -0.0232 -0.0095 Vr 0.0249 -0.9576 -0.2870 Vs -0.0024 -0.2872 0.9579 VolCenter 3.0033 11.5602 -3.6840 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0.00244356 -0.287158 0.95788 INFO: no Siemens slice order reversal detected (good!). TR=9850.00, TE=84.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999687, -0.0231588, -0.00949289) j_ras = (0.0249093, -0.957603, -0.287012) k_ras = (-0.00244356, -0.287158, 0.95788) writing to /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.voxel_space.bvecs /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs mri_probedicom --i /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm > /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dcminfo.dat cp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/gradients.txt /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs cp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/bvalues.txt /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.tmp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvals.tmp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals orientLAS /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 6.34232 mri_convert -oni 128 -onj 128 -onk 79 -oid -0.999687 -0.0231588 -0.00949289 -ojd -0.0249093 0.957603 0.287012 -okd -0.00244356 -0.287158 0.95788 -oc 2.95721 13.3333 -3.15258 -rt nearest /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 128 -onk 79 -oid -0.999687 -0.0231588 -0.00949289 -ojd -0.0249093 0.957603 0.287012 -okd -0.00244356 -0.287158 0.95788 -oc 2.95721 13.3333 -3.15258 -rt nearest /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999687, -0.0231588, -0.00949289) -> (-0.999687, -0.0231588, -0.00949289) normalizing out_j_direction: (-0.0249093, 0.957603, 0.287012) -> (-0.0249093, 0.957603, 0.287012) normalizing out_k_direction: (-0.00244356, -0.287158, 0.95788) -> (-0.00244356, -0.287158, 0.95788) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz... TR=9850.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999687, -0.0231588, -0.00949289) j_ras = (0.0249093, -0.957603, -0.287012) k_ras = (-0.00244356, -0.287158, 0.95788) Reslicing using nearest writing to /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz... INFO: found /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals, copying INFO: found /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs, converting to LAS mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.bvecs /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.bvals /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvals eddy_correct /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz 0 processing INTEL Image Exception : #63 :: No image files match: INTEL Image Exception : #22 :: Failed to read volume INTEL Error : No image files match: INTEL Failed to read volume INTEL Error : No image files match: INTEL processing MKL Image Exception : #63 :: No image files match: MKL Image Exception : #22 :: Failed to read volume MKL Error : No image files match: MKL Failed to read volume MKL Error : No image files match: MKL processing ERROR: Image Exception : #63 :: No image files match: ERROR: Image Exception : #22 :: Failed to read volume ERROR: Error : No image files match: ERROR: Failed to read volume ERROR: Error : No image files match: ERROR: processing /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Image Exception : #63 :: No image files match: /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Image Exception : #22 :: Failed to read volume /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Error : No image files match: /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Failed to read volume /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Error : No image files match: /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: processing undefined Image Exception : #63 :: No image files match: undefined Image Exception : #22 :: Failed to read volume undefined Error : No image files match: undefined Failed to read volume undefined Error : No image files match: undefined processing symbol: Image Exception : #63 :: No image files match: symbol: Image Exception : #22 :: Failed to read volume symbol: Error : No image files match: symbol: Failed to read volume symbol: Error : No image files match: symbol: processing mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Image Exception : #63 :: No image files match: mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Image Exception : #22 :: Failed to read volume mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Error : No image files match: mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Failed to read volume mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Error : No image files match: mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. processing Intel Image Exception : #63 :: No image files match: Intel Image Exception : #22 :: Failed to read volume Intel Error : No image files match: Intel Failed to read volume Intel Error : No image files match: Intel processing MKL Image Exception : #63 :: No image files match: MKL Image Exception : #22 :: Failed to read volume MKL Error : No image files match: MKL Failed to read volume MKL Error : No image files match: MKL processing FATAL Image Exception : #63 :: No image files match: FATAL Image Exception : #22 :: Failed to read volume FATAL Error : No image files match: FATAL Failed to read volume FATAL Error : No image files match: FATAL processing ERROR: Image Exception : #63 :: No image files match: ERROR: Image Exception : #22 :: Failed to read volume ERROR: Error : No image files match: ERROR: Failed to read volume ERROR: Error : No image files match: ERROR: processing Cannot Image Exception : #63 :: No image files match: Cannot Image Exception : #22 :: Failed to read volume Cannot Error : No image files match: Cannot Failed to read volume Cannot Error : No image files match: Cannot processing load Image Exception : #63 :: No image files match: load Image Exception : #22 :: Failed to read volume load Error : No image files match: load Failed to read volume load Error : No image files match: load processing libmkl_core.so. Image Exception : #63 :: No image files match: libmkl_core.so. Image Exception : #22 :: Failed to read volume libmkl_core.so. Error : No image files match: libmkl_core.so. Failed to read volume libmkl_core.so. Error : No image files match: libmkl_core.so. Image Exception : #63 :: No image files match: INTEL terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: INTEL /home1/jar269/fsl/bin/eddy_correct: line 103: 13578 Aborted (core dumped) fslmerge -t $output $full_list mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.norot xfmrot /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.ecclog /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.norot /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. 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R: Subscript out of range. ln -sf /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/data.nii.gz mri_convert --frame 0 1 2 3 4 5 6 7 8 9 /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/lowb.nii.gz mri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9 /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/lowb.nii.gz niiRead(): error opening file /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz... Linux librapet.med.yale.edu 3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Sun Jul 12 14:29:05 EDT 2020
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