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 <s0675...@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 > <ayend...@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 >>> <ayend...@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 >>>>> <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
