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Hello,
I’m running into an error in the longitudinal TRACULA pipeline that I’m not sure how to resolve. I saw this error in the message board but there was no resolution to the problem so I thought I’d ask again. I’ve successfully run the recon-all
longitudinal pipeline and am trying to run the trac-all –prep step with a longitudinal configuration file.
Here’s the error, it happens for both time points listed in my configuration file:
#@# Image corrections Thu Sep 27 12:59:31 CDT 2018
mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz
mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1...
crypt_gkey = *CyXds2s6sOqQ
Starting DICOMRead2()
dcmfile = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI
Ref Series No = 6
Found 2666 files, checking for dicoms
Found 2660 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 2
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 38
nslices = 70
ndcmfiles = 2660
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=10000.00, TE=57.70, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz...
crypt_gkey = *CyXds2s6sOqQ
mri_probedicom --i /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat
cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs
cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals
flip4fsl /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2
fslswapdim /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x -y z /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals
eddy_correct /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0000
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0005
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0006
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0007
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0008
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0009
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0010
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0011
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0012
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0013
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0014
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0015
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0016
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0017
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0018
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0019
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0020
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0021
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0022
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0023
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0024
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0025
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0026
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0027
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0028
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0029
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0030
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0031
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0032
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0033
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0034
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0035
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0036
processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0037
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.norot
xfmrot /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.ecclog /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.norot /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_eddy.nii.gz
mri_convert / /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/b0mag.nii.gz
mri_convert / /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/b0mag.nii.gz
corRead(): can't open file /COR-.info
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /...
crypt_gkey = *CyXds2s6sOqQ
Linux vis-1.mortimer 2.6.32-754.3.5.el6.x86_64 #1 SMP Tue Aug 14 20:46:41 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Sep 27 13:41:04 CDT 2018
#-------------------------------------
/sharedapps/LS/psych_imaging/freesurfer/5.3.0_9.19.18/bin/trac-preproc
#-------------------------------------
#@# Inter-subject registration (base template) Thu Sep 27 13:41:05 CDT 2018
cp /bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/mni2anatorig.mat /bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/anatorig2mni.mat /bigraid-03/LS/Data/istar/freesurfer/106/dmri/xfms
cp: cannot stat `/bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/mni2anatorig.mat': No such file or directory
cp: cannot stat `/bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/anatorig2mni.mat': No such file or directory
Linux vis-1.mortimer 2.6.32-754.3.5.el6.x86_64 #1 SMP Tue Aug 14 20:46:41 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Sep 27 13:41:05 CDT 2018
Here’s the contents of my configuration file:
setenv SUBJECTS_DIR /bigraid-03/LS/Data/istar/Freesurfer
setsubjlist= ( 106_day2.fs 106_6mo.fs )
set baselist = ( 106 106 )
set runlist = (1 2)
set dcmlist = ( /bigraid-03/LS/RawData/iSTAR/106_day2/106_day2/p*/e*/DTI_all/DTI/*.1 /bigraid-03/LS/RawData/iSTAR/106_6mo /106_6mo/p*/e*/DTI_all/DTI/*.1 )
set bvecfile = /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt
set bvalfile = /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt
set dob0 = 1
set b0mlist = None
set b0plist = None
set echospacing=None
set doeddy =1
set dorotbvecs =1
set thrbet = 0.5
set doregflt =0
set doregbbr =1
set doregmni =1
set mnitemp= $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
set dogregcvs = 0
set cvstemp =cvs_avg35
set cvstempdir = $FREESURFER_HOME/subjects
set usemaskanat =1
set pathlist = (lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.ccg_PP rh.ccg_PP lh.cab_PP rh.cab_PP )
set ncpts = (5 5 7 5 5 5 4 4)
set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
set nstick =2
set nburnin =200
set nsample = 7500
set nkeep = 5
set reinit =0
Thanks so much for your help!
Carissa
Carissa N. Weis, B.S.
Graduate Student
Affective Neuroscience Laboratory
University of Wisconsin-Milwaukee
cnweis@uwm.edu