Can you please send the text files instead of pasting them in the email? Thanks!

On Fri, 7 Dec 2012, s0675204 wrote:

Hello

I think I spoke to soon!

It ended with errors again.

I get the error message: "bvecs and bvals don't have the same number of entries"

I saw on some older messages on the mail-base you said that we need to check that the number of entries in the bvals is same as and bvecs is 3 times as much as the number of volumes. I have checked that this is the case

I am wondering if it is some formatting problem? there are no spaces at the end of the file. and there are no end of line markers either.

Please could you advise me? I have attached the files and also pasted the contents below

My config file is still the same (as pasted below) except I tried changing nb0 to 2

(# Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 2)

best wishes,

Prerona

========================================================= bvals:

0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800

bvecs:

0 0.99864840507507 0.01463935524225 0.01274211052805 0.85177010297775 0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873 0.51641523838043 0.46147873997688 0.54209464788436 0.44143822789192 0.52723878622055 0.4250853061676 0.51590526103973 0.43744987249374 0.50455766916275 0.05208261311054 0.06073396280407 0.00979638285934 0 0.99864840507507 0.01463935524225 0.01274211052805 0.85177010297775 0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873 0.51641523838043 0.46147873997688 0.54209464788436 0.44143822789192 0.52723878622055 0.4250853061676 0.51590526103973 0.43744987249374 0.50455766916275 0.05208261311054 0.06073396280407 0.00979638285934 0 -0.00687454920262 0.96709138154983 0.62002921104431 0.52092331647872 0.18501849472522 -0.42448142170906 -0.44344407320022 0.15539556741714 0.60610836744308 0.88347893953323 0.71210372447967 0.30400663614273 -0.23736105859279 -0.70398008823394 -0.85636389255523 -0.73376137018203 -0.22848516702652 -0.00803200621157 0.51328992843627 0.93218487501144 0 -0.00687454920262 0.96709138154983 0.62002921104431 0.52092331647872 0.18501849472522 -0.42448142170906 -0.44344407320022 0.15539556741714 0.60610836744308 0.88347893953323 0.71210372447967 0.30400663614273 -0.23736105859279 -0.70398008823394 -0.85636389255523 -0.73376137018203 -0.22848516702652 -0.00803200621157 0.51328992843627 0.93218487501144 0 0.05151799321174 -0.2540076971054 -0.78447526693344 0.05591572076082 -0.46734625101089 -0.3037790954113 0.31549325585365 0.5914282798767 0.60493636131286 0.08063688874244 -0.44614082574844 -0.84422290325164 -0.81589156389236 -0.56895911693573 -0.02196817658841 0.51983833312988 0.83259600400924 0.99861049652099 0.85606354475021 0.36184993386268 0 0.05151799321174 -0.2540076971054 -0.78447526693344 0.05591572076082 -0.46734625101089 -0.3037790954113 0.31549325585365 0.5914282798767 0.60493636131286 0.08063688874244 -0.44614082574844 -0.84422290325164 -0.81589156389236 -0.56895911693573 -0.02196817658841 0.51983833312988 0.83259600400924 0.99861049652099 0.85606354475021 0.36184993386268 On 7 December 2012 14:08, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

...

Great, I love easy problems :)

On Fri, 7 Dec 2012, s0675204 wrote:

...

Thank you! It's chugging away now

best wishes,

Prerona

On 7 December 2012 13:46, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

...

Hi Prerona - You need to uncomment the bvecfile and bvalfile definitions in your configuration file.

Hope this helps, a.y

On Fri, 7 Dec 2012, s0675204 wrote:

...

Hello

I am trying to run Tracula on a set of dicoms files. I have run recon-all previously. I am getting a message trac-preproc exited with ERRORS

Please can anyone advise me on this? I have listed all the details (command, error/output, config file) below

Thank you so much for your help

best wishes,

Prerona

DETAILS

command used: trac-all -prep -c ./scripts/dmrirc_single_subject

========================================= error message

========================================= canlilab@112-205:~/SBU/data/tracula$ trac-all -prep -c ./scripts/dmrirc_single_subject INFO: SUBJECTS_DIR is /home/canlilab/SBU/data/recon_output INFO: Diffusion root is /home/canlilab/SBU/data/tracula Actual FREESURFER_HOME /home/canlilab/freesurfer trac-preproc -c /home/canlilab/SBU/data/tracula/00075/scripts/dmrirc.local -log /home/canlilab/SBU/data/tracula/00075/scripts/trac-all.log -cmd /home/canlilab/SBU/data/tracula/00075/scripts/trac-all.cmd #------------------------------------- /home/canlilab/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Dec 7 10:42:30 EST 2012 mri_convert /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz mri_convert /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm... Getting Series No INFO: Found 44 files in /home/canlilab/SBU/data/dti_dicoms/00075 INFO: Scanning for Series Number 7 Scanning Directory INFO: found 42 files in series INFO: loading series header info.

RunNo = 6 WARNING: Run 1 appears to be truncated Files Found: 42, Files Expected (lRep+1): 2 FileName /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName S790_P72_TC Date and time StudyDate 20120502 StudyTime 120741.390000 SeriesTime 125649.953000 AcqTime 125626.150000 Acquisition parameters PulseSeq ep_b0 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 93 InversionTime -1 RepetitionTime 5500 PhEncFOV 220 ReadoutFOV 220 Image information RunNo 6 SeriesNo 7 ImageNo 1 NImageRows 896 NImageCols 896 NFrames 42 SliceArraylSize 40 IsMosaic 1 ImgPos 772.3238 773.0634 185.5347 VolRes 1.7188 1.7188 3.0000 VolDim 128 128 40 Vc -0.9983 0.0151 -0.0555 Vr -0.0000 -0.9648 -0.2629 Vs -0.0575 -0.2625 0.9632 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 40), nframes = 42, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 5500, TR = 5500 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;

FileName /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName S790_P72_TC Date and time StudyDate 20120502 StudyTime 120741.390000 SeriesTime 125649.953000 AcqTime 125626.150000 Acquisition parameters PulseSeq ep_b0 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 93 InversionTime -1 RepetitionTime 5500 PhEncFOV 220 ReadoutFOV 220 Image information RunNo 6 SeriesNo 7 ImageNo 1 NImageRows 896 NImageCols 896 NFrames 42 SliceArraylSize 40 IsMosaic 1 ImgPos 113.4156 146.2544 -24.5854 VolRes 1.7188 1.7188 3.0000 VolDim 128 128 40 Vc -0.9983 0.0151 -0.0555 Vr -0.0000 -0.9648 -0.2629 Vs -0.0575 -0.2625 0.9632 VolCenter 0.1478 26.0388 -1.8116 TransferSyntaxUID 1.2.840.10008.1.2.1 sagrev = 0, correv =0, trarev = 0 Vs = -0.0574949 -0.262456 0.963229 INFO: no Siemens slice order reversal detected (good!). TR=5500.00, TE=93.00, TI=-1.00, flip angle=90.00 i_ras = (-0.998346, 0.0151149, -0.0554726) j_ras = (-3.31902e-08, -0.964826, -0.262891) k_ras = (-0.0574949, -0.262456, 0.963229) writing to /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz... mri_probedicom --i /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm

...

/home/canlilab/SBU/data/tracula/00075/dmri/dcminfo.dat

flip4fsl /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8.86231 fslswapdim /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz x -y z /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz mv -f /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs /home/canlilab/SBU/data/tracula/00075/dmri/bvecs mv: cannot stat `/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux 112-205.psy.sunysb.edu 2.6.32-279.5.2.el6.x86_64 #1 SMP Fri Aug 24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 7 10:42:51 EST 2012

config file:

# # dmrirc.example # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2011/05/24 06:47:12 $ # $Revision: 1.3.2.3 $ # # Copyright © 2011 The General Hospital Corporation (Boston MA) "MGH" # # Terms and conditions for use reproduction distribution and contribution # are found in the 'FreeSurfer Software License Agreement' contained # in the file 'LICENSE' found in the FreeSurfer distribution and here: # # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense # # Reporting: freesurfer@nmr.mgh.harvard.edu # #

# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /path/to/recons/of/ducks

# Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = $pre_data/tracula

# Subject IDs # set subjlist = (00075 00104 00122 00200 00308 00369 00387 00400 00422 00452 00518 00568 00587 00624 00636 00686 00698 00727 00909 00926 00933 00943 00983 00992 01049 01121 01329 01450 01509 01531 01678 01735 01746 01809 01843 01917 10039 10056 10089 10165 10171 10227 10238 10263 10314 10320 10326 10349 10407 10431 10435 10458 10477 10499 10500 10636 10750 11209 12210 12357 12472 12645 13493 13958 14302 14481 14530 15329 15345 15864 16654 17267 17478 18337 18422 18530 19259 19377 19725 20071 20383 21413 23846 24115 24531 24781 25962 26314 26475 28822 30510 30571 30927 31034 31049 31237 31437 31471 31531 32131 32162 32222)

# In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102)

# Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist these can be in other image format # but then bvecfile bvalfile and nb0 must be specified (see below) #

set dcmroot = $pre_data/dti_dicoms set dcmlist = (00075/data_1.dcm \ 00104/data_1.dcm \ 00122/data_1.dcm \ 00200/data_1.dcm \ 00308/data_1.dcm \ 00369/data_1.dcm \ 00387/data_1.dcm \ 00400/data_1.dcm \ 00422/data_1.dcm \ 00452/data_1.dcm \ 00518/data_1.dcm \ 00568/data_1.dcm \ 00587/data_1.dcm \ 00624/data_1.dcm \ 00636/data_1.dcm \ 00686/data_1.dcm \ 00698/data_1.dcm \ 00727/data_1.dcm \ 00909/data_1.dcm \ 00926/data_1.dcm \ 00933/data_1.dcm \ 00943/data_1.dcm \ 00983/data_1.dcm \ 00992/data_1.dcm \ 01049/data_1.dcm \ 01121/data_1.dcm \ 01329/data_1.dcm \ 01450/data_1.dcm \ 01509/data_1.dcm \ 01531/data_1.dcm \ 01678/data_1.dcm \ 01735/data_1.dcm \ 01746/data_1.dcm \ 01809/data_1.dcm \ 01843/data_1.dcm \ 01917/data_1.dcm \ 10039/data_1.dcm \ 10056/data_1.dcm \ 10089/data_1.dcm \ 10165/data_1.dcm \ 10171/data_1.dcm \ 10227/data_1.dcm \ 10238/data_1.dcm \ 10263/data_1.dcm \ 10314/data_1.dcm \ 10320/data_1.dcm \ 10326/data_1.dcm \ 10349/data_1.dcm \ 10407/data_1.dcm \ 10431/data_1.dcm \ 10435/data_1.dcm \ 10458/data_1.dcm \ 10477/data_1.dcm \ 10499/data_1.dcm \ 10500/data_1.dcm \ 10636/data_1.dcm \ 10750/data_1.dcm \ 11209/data_1.dcm \ 12210/data_1.dcm \ 12357/data_1.dcm \ 12472/data_1.dcm \ 12645/data_1.dcm \ 13493/data_1.dcm \ 13958/data_1.dcm \ 14302/data_1.dcm \ 14481/data_1.dcm \ 14530/data_1.dcm \ 15329/data_1.dcm \ 15345/data_1.dcm \ 15864/data_1.dcm \ 16654/data_1.dcm \ 17267/data_1.dcm \ 17478/data_1.dcm \ 18337/data_1.dcm \ 18422/data_1.dcm \ 18530/data_1.dcm \ 19259/data_1.dcm \ 19377/data_1.dcm \ 19725/data_1.dcm \ 20071/data_1.dcm \ 20383/data_1.dcm \ 21413/data_1.dcm \ 23846/data_1.dcm \ 24115/data_1.dcm \ 24531/data_1.dcm \ 24781/data_1.dcm \ 25962/data_1.dcm \ 26314/data_1.dcm \ 26475/data_1.dcm \ 28822/data_1.dcm \ 30510/data_1.dcm \ 30571/data_1.dcm \ 30927/data_1.dcm \ 31034/data_1.dcm \ 31049/data_1.dcm \ 31237/data_1.dcm \ 31437/data_1.dcm \ 31471/data_1.dcm \ 31531/data_1.dcm \ 32131/data_1.dcm \ 32162/data_1.dcm \ 32222/data_1.dcm)

# Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format one row for each volume in the diffusion data set # Default: Read from DICOM header # #set bvecfile = $pre_data/DTI_Analysis/00075/bvecs.txt

# Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format one value for each volume in the diffusion data set # Default: Read from DICOM header # #set bvalfile = $pre_data/DTI_Analysis/00075/bvals.txt

# Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 1

# Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # set dob0 = 0

# Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # #set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)

# Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # #set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm)

# Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # #set echospacing = 0.7

# Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1

# Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1

# Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.5

# Perform diffusion-to-T1 registration by flirt? # Default: 1 (yes) # set doregflt = 1

# Perform diffusion-to-T1 registration by bbregister? # Default: 0 (no) # set doregbbr = 0

# MNI template (the only option for inter-subject registration in this version) # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

# Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1

# Paths to reconstruct # Default: All paths in the atlas # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP )

# Number of path control points # Default: 5 # set ncpts = 5

# List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt

# Use long (more descriptive) directory hierarchy for saving path distributions? # By default paths distributions are saved directly under $subjectname/dpath # Default: 0 (no) # set dopathsubdirs = 0

# Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200

# Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 5000 # set nsample = 5000

# Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 ==============================================

---

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