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 <ayend...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis < > alandarkene...@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.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 * > > *al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> * > *afran...@mclean.harvard.edu <afran...@mclean.harvard.edu>* > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School* *Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging* *Massachusetts General Hospital* *149, 13th street, Charlestown, MA* *al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> * *afran...@mclean.harvard.edu <afran...@mclean.harvard.edu>*
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