External Email - Use Caution
Dear Anastasia -
I tried running tracula preproc. However, it gave me an error message. Could you please shed some light on this?
Thank you,
Alan
[airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC INFO: Diffusion root is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6 trac-preproc -c /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/dmrirc.local -log /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.log -cmd /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable6/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Oct 15 10:01:10 EDT 2019 mri_convert --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals orientLAS /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -18.7806 mri_convert -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.996936, 0.0343122, -0.0703008) -> (-0.996936, 0.0343122, -0.0703008) normalizing out_j_direction: (0.0173889, 0.973389, 0.228497) -> (0.0173889, 0.973389, 0.228497) normalizing out_k_direction: (-0.0762703, -0.226574, 0.971003) -> (-0.0762703, -0.226574, 0.971003) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) Reslicing using nearest writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz... INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals, copying INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs, converting to LAS mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals eddy_correct /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz 0 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0000 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0001 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0002 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0003 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0004 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0005 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0006 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0007 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0008 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0009 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0010 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0011 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0012 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0013 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0014 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0015 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0016 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0017 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0018 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0019 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0020 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0021 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0022 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0023 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0024 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0025 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0026 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0027 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0028 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0029 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0030 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0031 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0032 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0033 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0034 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0035 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0036 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0037 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0038 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0039 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0040 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0041 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0042 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0043 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0044 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0045 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0046 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0047 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0048 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0049 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0050 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0051 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0052 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0053 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0054 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0055 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0056 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0057 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0058 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0059 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0060 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0061 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0062 mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot xfmrot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.ecclog /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. ln -sf /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/data.nii.gz mri_convert --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz mri_convert.bin --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) keeping frame 63 ERROR: valid frame numbers are between 0 and 62 Linux airhunger.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Oct 15 10:17:55 EDT 2019
Hi Alan - It looks like it may be due to a mismatch between the bvals/bvecs files and the number of volumes in your DWI data. I think it's expecting to find a b=0 volume as the 64th volume, but your DWI nifti has only 63 volumes.
a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alan Francis alandarkenergy@gmail.com Sent: Tuesday, October 15, 2019 10:26:32 AM To: Freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula question
External Email - Use Caution
Dear Anastasia -
I tried running tracula preproc. However, it gave me an error message. Could you please shed some light on this?
Thank you,
Alan
[airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC INFO: Diffusion root is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6 trac-preproc -c /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/dmrirc.local -log /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.log -cmd /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable6/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Oct 15 10:01:10 EDT 2019 mri_convert --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals orientLAS /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -18.7806 mri_convert -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.996936, 0.0343122, -0.0703008) -> (-0.996936, 0.0343122, -0.0703008) normalizing out_j_direction: (0.0173889, 0.973389, 0.228497) -> (0.0173889, 0.973389, 0.228497) normalizing out_k_direction: (-0.0762703, -0.226574, 0.971003) -> (-0.0762703, -0.226574, 0.971003) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) Reslicing using nearest writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz... INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals, copying INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs, converting to LAS mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals eddy_correct /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz 0 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0000 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0001 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0002 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0003 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0004 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0005 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0006 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0007 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0008 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0009 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0010 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0011 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0012 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0013 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0014 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0015 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0016 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0017 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0018 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0019 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0020 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0021 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0022 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0023 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0024 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0025 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0026 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0027 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0028 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0029 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0030 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0031 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0032 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0033 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0034 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0035 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0036 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0037 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0038 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0039 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0040 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0041 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0042 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0043 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0044 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0045 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0046 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0047 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0048 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0049 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0050 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0051 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0052 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0053 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0054 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0055 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0056 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0057 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0058 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0059 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0060 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0061 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0062 mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot xfmrot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.ecclog /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. ln -sf /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/data.nii.gz mri_convert --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz mri_convert.bin --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) keeping frame 63 ERROR: valid frame numbers are between 0 and 62 Linux airhunger.nmr.mgh.harvard.eduhttp://airhunger.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Oct 15 10:17:55 EDT 2019
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD Instructor in Psychiatry Harvard Medical School
Louis V. Gerstner III scholar Martinos Center for Biomedical Imaging Massachusetts General Hospital 149, 13th street, Charlestown, MA alanf@bwh.harvard.edumailto:ezra_wegbreit@brown.edu afrancis@mclean.harvard.edumailto:afrancis@mclean.harvard.edu
External Email - Use Caution
Thanks Anastasia. That is exactly what happened and we have fixed it.
best,
Alan
On Tue, Oct 15, 2019 at 5:37 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Hi Alan - It looks like it may be due to a mismatch between the bvals/bvecs files and the number of volumes in your DWI data. I think it's expecting to find a b=0 volume as the 64th volume, but your DWI nifti has only 63 volumes.
a.y
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Tuesday, October 15, 2019 10:26:32 AM *To:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula question
External Email - Use CautionDear Anastasia -
I tried running tracula preproc. However, it gave me an error message. Could you please shed some light on this?
Thank you,
Alan
[airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC INFO: Diffusion root is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6 trac-preproc -c /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/dmrirc.local -log /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.log -cmd /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable6/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Oct 15 10:01:10 EDT 2019 mri_convert --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals orientLAS /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -18.7806 mri_convert -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.996936, 0.0343122, -0.0703008) -> (-0.996936, 0.0343122, -0.0703008) normalizing out_j_direction: (0.0173889, 0.973389, 0.228497) -> (0.0173889, 0.973389, 0.228497) normalizing out_k_direction: (-0.0762703, -0.226574, 0.971003) -> (-0.0762703, -0.226574, 0.971003) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) Reslicing using nearest writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz... INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals, copying INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs, converting to LAS mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals eddy_correct /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz 0 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0000 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0001 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0002 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0003 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0004 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0005 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0006 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0007 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0008 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0009 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0010 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0011 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0012 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0013 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0014 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0015 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0016 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0017 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0018 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0019 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0020 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0021 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0022 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0023 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0024 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0025 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0026 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0027 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0028 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0029 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0030 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0031 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0032 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0033 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0034 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0035 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0036 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0037 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0038 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0039 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0040 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0041 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0042 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0043 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0044 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0045 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0046 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0047 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0048 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0049 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0050 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0051 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0052 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0053 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0054 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0055 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0056 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0057 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0058 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0059 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0060 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0061 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0062 mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot xfmrot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.ecclog /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. ln -sf /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/data.nii.gz mri_convert --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz mri_convert.bin --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) keeping frame 63 ERROR: valid frame numbers are between 0 and 62 Linux airhunger.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Oct 15 10:17:55 EDT 2019
-- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
Alan N. Francis PhD Instructor in Psychiatry Harvard Medical School *
Louis V. Gerstner III scholar Martinos Center for Biomedical Imaging *
*Massachusetts General Hospital *
*149, 13th street, Charlestown, MA *
*alanf@bwh.harvard.edu ezra_wegbreit@brown.edu * *afrancis@mclean.harvard.edu afrancis@mclean.harvard.edu*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Alan Francis -
Yendiki, Anastasia