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<http://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<mailto:ezra_wegbr...@brown.edu>
afran...@mclean.harvard.edu<mailto:afran...@mclean.harvard.edu>
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