Hello
My trac- preproc has completed. However, I am confused about the status message. It says:
#------------------------------------- trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012 ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387
Does this mean it was completed succesfully for everyone or everyone but that 00387 person?
Is there any way I can verify this?
thank you so much for your help
best wishes,
Prerona
On 8 December 2012 13:38, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
In your dmrirc, you define multiple subjects, but only one bvecfile and one bvalfile that are used for all subjects.
On Sat, 8 Dec 2012, s0675204 wrote:
the values are the same but each subject has an individual bvec & bval file. so it depends on how the script will read it?
On 8 December 2012 00:03, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Are the bvecs/bvals not the same for all subjects?
On Fri, 7 Dec 2012, s0675204 wrote:
oh! i thought this was how these were meant to be! i will do that. sadly i left the lab and came home for the day but i will try it as soon as i am back and let you know! thank you so much! do we have to do this for each subject or just one time?
On 7 December 2012 23:51, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
I see. Can you try formatting them in columns (1 column for the bvals and 3 columns for the bvecs)?
On Fri, 7 Dec 2012, s0675204 wrote:
yes! these are the original files
well these are the files i pointed to in my config file. and i think the script copies them over to the dmrirc folder?
best wishes,
Prerona
On 7 December 2012 23:38, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote: > > > > > Yes, I can see that each of the bvecs/bvals files is one long line. > Was > that > the case for the original files that you specified in the dmrirc? > > > On Fri, 7 Dec 2012, s0675204 wrote: > >> Hi Anastasia >> >> I had attached the files, but maybe they did not go through to the >> mailing list? So I am sending them to your email id. Hope this is >> okay >> >> best wishes, >> >> Prerona >> >> >> >> ---------- Forwarded message ---------- >> From: s0675204 s0675204@sms.ed.ac.uk >> Date: 7 December 2012 19:44 >> Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited with >> ERRORS >> To: freesurfer@nmr.mgh.harvard.edu >> >> >> 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 >>>>>> ============================================== >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to >>>>> whom >>>>> it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error >>>>> and >>>>> the >>>>> e-mail >>>>> contains patient information, please contact the Partners >>>>> Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent >>>>> to >>>>> you >>>>> in >>>>> error >>>>> but does not contain patient information, please contact the >>>>> sender >>>>> and >>>>> properly >>>>> dispose of the e-mail. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >
I'm guessing that this shows up in the scripts/trac-all.log of a particular subject? Then it applies to that subject.
On Mon, 10 Dec 2012, s0675204 wrote:
Hello
My trac- preproc has completed. However, I am confused about the status message. It says:
#------------------------------------- trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012 ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387
Does this mean it was completed succesfully for everyone or everyone but that 00387 person?
Is there any way I can verify this?
thank you so much for your help
best wishes,
Prerona
On 8 December 2012 13:38, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
In your dmrirc, you define multiple subjects, but only one bvecfile and one bvalfile that are used for all subjects.
On Sat, 8 Dec 2012, s0675204 wrote:
the values are the same but each subject has an individual bvec & bval file. so it depends on how the script will read it?
On 8 December 2012 00:03, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Are the bvecs/bvals not the same for all subjects?
On Fri, 7 Dec 2012, s0675204 wrote:
oh! i thought this was how these were meant to be! i will do that. sadly i left the lab and came home for the day but i will try it as soon as i am back and let you know! thank you so much! do we have to do this for each subject or just one time?
On 7 December 2012 23:51, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
I see. Can you try formatting them in columns (1 column for the bvals and 3 columns for the bvecs)?
On Fri, 7 Dec 2012, s0675204 wrote:
> yes! these are the original files > > well these are the files i pointed to in my config file. and i think > the script copies them over to the dmrirc folder? > > best wishes, > > Prerona > > > On 7 December 2012 23:38, Anastasia Yendiki > ayendiki@nmr.mgh.harvard.edu wrote: >> >> >> >> >> Yes, I can see that each of the bvecs/bvals files is one long line. >> Was >> that >> the case for the original files that you specified in the dmrirc? >> >> >> On Fri, 7 Dec 2012, s0675204 wrote: >> >>> Hi Anastasia >>> >>> I had attached the files, but maybe they did not go through to the >>> mailing list? So I am sending them to your email id. Hope this is >>> okay >>> >>> best wishes, >>> >>> Prerona >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: s0675204 s0675204@sms.ed.ac.uk >>> Date: 7 December 2012 19:44 >>> Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited with >>> ERRORS >>> To: freesurfer@nmr.mgh.harvard.edu >>> >>> >>> 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 >>>>>>> ============================================== >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom >>>>>> it >>>>>> is >>>>>> addressed. If you believe this e-mail was sent to you in error >>>>>> and >>>>>> the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners >>>>>> Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent >>>>>> to >>>>>> you >>>>>> in >>>>>> error >>>>>> but does not contain patient information, please contact the >>>>>> sender >>>>>> and >>>>>> properly >>>>>> dispose of the e-mail. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >> > >
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
s0675204