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 <ayend...@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 >> <ayend...@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 >>>> <ayend...@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 >>>>>> <ayend...@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 <s0675...@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 >>>>>>>> <ayend...@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 >>>>>>>>>> <ayend...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
