Hello,
thank you for your help with the first steps of running Tracula.
I was trying to run trac-all step 3 (paths), but was getting an error with the mergedph1samples file. I saw on the mailbase that you have suggested to run bedpost directly to fix this
I have 3 questions about this:
1) do I need to delete any of the (temporary?) files or folders created by trac-all step 2 before running bedpost
2) should I run bedpost INSTEAD of trac-all step 2 for the remaining subjects?
3) you have suggested on the list to run bedpost as: bedpostx /usr/local/freesurfer/subjects/C001/dmri is this the same dmri folder as created by tracula step 1 (for each subject)
Thank you so much for your help with this - I really appreciate it
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. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>> >> >> >