Tue Dec 28 14:57:33 EST 2021 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/trac-all -prep -c dmricr.tutorial Subject AG007_0425_T1_LAZAR SUBJECTS_DIR /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/7.2.0 Actual FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/7.2.0 build-stamp.txt: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b ek526 launchpad.nmr.mgh.harvard.edu Linux launchpad.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked unlimited maxproc 127905 maxlocks unlimited maxsignal 127905 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32778768 2210892 21093228 480552 9474648 29685468 Swap: 67108856 1116036 65992820 ######################################## Program versions: trac-all 7.2.0 mri_convert --all-info ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-19:57:33-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 FLIRT version 6.0 bbregister 7.2.0 mri_cvs_register 7.2.0 ProgramName: dmri_motion ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_motion --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-19:57:33-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_train ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_train --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-19:57:33-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_paths ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_paths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-19:57:34-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_pathstats ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_pathstats --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-19:57:34-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_mergepaths ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_mergepaths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-19:57:34-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_group ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_group --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-19:57:34-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 New invocation of trac-preproc ek526 compute-0-122.nmr.mgh.harvard.edu Linux compute-0-122.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 127909 maxlocks unlimited maxsignal 127909 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32778856 1215328 30141436 279688 1422092 30859760 Swap: 67108860 823864 66284996 #------------------------------------- /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Dec 28 14:57:40 EST 2021 rm -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (0.0507603, -0.970633, -0.235151) k_ras = (0.01654, -0.234605, 0.97195) writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz... rm -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs.tmp mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals orientLAS /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 mri_convert -oni 116 -onj 116 -onk 69 -oid -0.998574 -0.0532259 0.00414569 -ojd -0.0507603 0.970633 0.235151 -okd 0.01654 -0.234605 0.97195 -oc 6.85592 39.8861 -14.0201 -rt nearest /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 116 -onj 116 -onk 69 -oid -0.998574 -0.0532259 0.00414569 -ojd -0.0507603 0.970633 0.235151 -okd 0.01654 -0.234605 0.97195 -oc 6.85592 39.8861 -14.0201 -rt nearest /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz normalizing out_i_direction: (-0.998574, -0.0532259, 0.00414569) -> (-0.998574, -0.0532259, 0.00414569) normalizing out_j_direction: (-0.0507603, 0.970633, 0.235151) -> (-0.0507603, 0.970632, 0.235151) normalizing out_k_direction: (0.01654, -0.234605, 0.97195) -> (0.01654, -0.234605, 0.97195) reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (0.0507603, -0.970633, -0.235151) k_ras = (0.01654, -0.234605, 0.97195) Reslicing using nearest writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz... INFO: found /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals, copying INFO: found /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.bvecs /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvecs mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.bvals /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvals mri_convert --frame 0 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz mri_convert --frame 0 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (-0.0507603, 0.970632, 0.235151) k_ras = (0.01654, -0.234605, 0.97195) keeping frame 0 writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz... bet /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las_brain.nii.gz -m -f 0.3 eddy_openmp --imain=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz --mask=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvecs --bvals=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvals --acqp=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/acqp.txt --index=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/index.txt --data_is_shelled --out=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi EddyInputError: Error when attempting to read --index file /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/index.txt Terminating program Linux compute-0-122.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Dec 28 14:58:22 EST 2021 New invocation of trac-all Tue Dec 28 15:02:22 EST 2021 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/trac-all -prep -c dmricr.tutorial Subject AG007_0425_T1_LAZAR SUBJECTS_DIR /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/7.2.0 Actual FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/7.2.0 build-stamp.txt: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b ek526 launchpad.nmr.mgh.harvard.edu Linux launchpad.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked unlimited maxproc 127905 maxlocks unlimited maxsignal 127905 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32778768 2215104 21009728 480584 9553936 29681368 Swap: 67108856 1116036 65992820 ######################################## Program versions: trac-all 7.2.0 mri_convert --all-info ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-20:02:22-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 FLIRT version 6.0 bbregister 7.2.0 mri_cvs_register 7.2.0 ProgramName: dmri_motion ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_motion --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-20:02:22-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_train ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_train --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-20:02:22-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_paths ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_paths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-20:02:22-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_pathstats ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_pathstats --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-20:02:22-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_mergepaths ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_mergepaths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-20:02:22-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_group ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_group --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/28-20:02:22-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 New invocation of trac-preproc ek526 compute-0-92.nmr.mgh.harvard.edu Linux compute-0-92.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 127909 maxlocks unlimited maxsignal 127909 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32778928 1436296 29831172 261232 1511460 30657256 Swap: 67108860 1334404 65774456 #------------------------------------- /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Dec 28 15:02:27 EST 2021 rm -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (0.0507603, -0.970633, -0.235151) k_ras = (0.01654, -0.234605, 0.97195) writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz... rm -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs.tmp mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals orientLAS /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 mri_convert -oni 116 -onj 116 -onk 69 -oid -0.998574 -0.0532259 0.00414569 -ojd -0.0507603 0.970633 0.235151 -okd 0.01654 -0.234605 0.97195 -oc 6.85592 39.8861 -14.0201 -rt nearest /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 116 -onj 116 -onk 69 -oid -0.998574 -0.0532259 0.00414569 -ojd -0.0507603 0.970633 0.235151 -okd 0.01654 -0.234605 0.97195 -oc 6.85592 39.8861 -14.0201 -rt nearest /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz normalizing out_i_direction: (-0.998574, -0.0532259, 0.00414569) -> (-0.998574, -0.0532259, 0.00414569) normalizing out_j_direction: (-0.0507603, 0.970633, 0.235151) -> (-0.0507603, 0.970632, 0.235151) normalizing out_k_direction: (0.01654, -0.234605, 0.97195) -> (0.01654, -0.234605, 0.97195) reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (0.0507603, -0.970633, -0.235151) k_ras = (0.01654, -0.234605, 0.97195) Reslicing using nearest writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz... INFO: found /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals, copying INFO: found /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.bvecs /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvecs mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.bvals /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvals mri_convert --frame 0 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz mri_convert --frame 0 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (-0.0507603, 0.970632, 0.235151) k_ras = (0.01654, -0.234605, 0.97195) keeping frame 0 writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz... bet /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las_brain.nii.gz -m -f 0.3 eddy_openmp --imain=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz --mask=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvecs --bvals=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvals --acqp=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/acqp.txt --index=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/index.txt --data_is_shelled --out=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi EddyInputError: Error when attempting to read --index file /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/index.txt Terminating program Linux compute-0-92.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Dec 28 15:03:25 EST 2021 New invocation of trac-all Thu Dec 30 16:58:24 EST 2021 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/trac-all -prep -c dmricr.tutorial Subject AG007_0425_T1_LAZAR SUBJECTS_DIR /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/7.2.0 Actual FREESURFER_HOME /autofs/vast/freesurfer/centos7_x86_64/7.2.0 build-stamp.txt: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b ek526 launchpad.nmr.mgh.harvard.edu Linux launchpad.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked unlimited maxproc 127905 maxlocks unlimited maxsignal 127905 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32778768 2184628 21434332 488596 9159808 29703688 Swap: 67108856 1079940 66028916 ######################################## Program versions: trac-all 7.2.0 mri_convert --all-info ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/30-21:58:24-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 FLIRT version 6.0 bbregister 7.2.0 mri_cvs_register 7.2.0 ProgramName: dmri_motion ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_motion --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/30-21:58:25-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_train ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_train --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/30-21:58:25-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_paths ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_paths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/30-21:58:25-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_pathstats ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_pathstats --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/30-21:58:25-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_mergepaths ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_mergepaths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/30-21:58:25-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_group ProgramArguments: /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/dmri_group --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/12/30-21:58:25-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: ek526 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 New invocation of trac-preproc ek526 compute-0-47.nmr.mgh.harvard.edu Linux compute-0-47.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 127909 maxlocks unlimited maxsignal 127909 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32778856 1225148 29852044 348996 1701664 30780576 Swap: 67108860 1230120 65878740 #------------------------------------- /autofs/vast/freesurfer/centos7_x86_64/7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Dec 30 16:58:32 EST 2021 rm -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/DTI/dti_two.nii... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (0.0507603, -0.970633, -0.235151) k_ras = (0.01654, -0.234605, 0.97195) writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz... rm -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs.tmp mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals.tmp /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals orientLAS /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 mri_convert -oni 116 -onj 116 -onk 69 -oid -0.998574 -0.0532259 0.00414569 -ojd -0.0507603 0.970633 0.235151 -okd 0.01654 -0.234605 0.97195 -oc 6.85592 39.8861 -14.0201 -rt nearest /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 116 -onj 116 -onk 69 -oid -0.998574 -0.0532259 0.00414569 -ojd -0.0507603 0.970633 0.235151 -okd 0.01654 -0.234605 0.97195 -oc 6.85592 39.8861 -14.0201 -rt nearest /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz normalizing out_i_direction: (-0.998574, -0.0532259, 0.00414569) -> (-0.998574, -0.0532259, 0.00414569) normalizing out_j_direction: (-0.0507603, 0.970633, 0.235151) -> (-0.0507603, 0.970632, 0.235151) normalizing out_k_direction: (0.01654, -0.234605, 0.97195) -> (0.01654, -0.234605, 0.97195) reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.nii.gz... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (0.0507603, -0.970633, -0.235151) k_ras = (0.01654, -0.234605, 0.97195) Reslicing using nearest writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz... INFO: found /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvals, copying INFO: found /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.bvecs /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvecs mv -f /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.1.bvals /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvals mri_convert --frame 0 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz mri_convert --frame 0 /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz reading from /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz... TR=7500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998574, -0.0532259, 0.00414569) j_ras = (-0.0507603, 0.970632, 0.235151) k_ras = (0.01654, -0.234605, 0.97195) keeping frame 0 writing to /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz... bet /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las.nii.gz /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las_brain.nii.gz -m -f 0.3 eddy_openmp --imain=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.nii.gz --mask=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvecs --bvals=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi_orig_las.bvals --acqp=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/acqp.txt --index=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/index.txt --data_is_shelled --out=/autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/dwi EddyInputError: Error when attempting to read --index file /autofs/space/metta_001/users/DTIanalysis/Subjects_DTI_t1t2/Recon/AG007_0425_T1_LAZAR/dmri/index.txt Terminating program Linux compute-0-47.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Dec 30 16:59:29 EST 2021