Thank you so much! All (?) makes sense now that I am looking at the log files.
It has actually only processed 6 (out of 102). Now I am trying to figure out why it skipped the ones it did
best wishes,
Prerona
On 10 December 2012 20:33, s0675204 s0675204@sms.ed.ac.uk wrote:
okay. i will look through the logs for all the subjects and check! Thanks so much
best wishes,
Prerona
On 10 December 2012 20:00, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Which subject was running at the time? What shows up in the console will also be in trac-all.log. If you're not sure you should grep all subject's logs for errors.
On Mon, 10 Dec 2012, s0675204 wrote:
it was just on the screen when the program ended (on the console)?
best wishes,
Prerona
On 10 December 2012 19:54, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
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. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >> > >