Hello I have one more problem. Some of the subjects completed step 1 (preprocessing) successfully according to the logs & there are no error messages. However, when I try to run the bedpost step on these subjects, I get an error message saying there is no data.nii.gz file in the dmrirc There is however a dwi.nii.gz file present
Can you help me understand what happened here? Has something gone wrong? How can I fix it? Thank you so much for your help! best wishes, Prerona On 17 December 2012 12:48, s0675204 <s0675...@sms.ed.ac.uk> wrote: > Hello > > I have been running trac-paths, and thought it finishes with a message > saying no errors, > I get an error saying ERROR: Degenerate spline segment in the > intermediate message logs > > Also I looked at the result using this command: > freeview -v $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_FA.nii.gz \ > > $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' > \ > > $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/rh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' > & > > but it had only traced a part of the trac on one side and nothing on > the other side > > Can you help me understand what went wrong and how to fix it? > > Thank you so much for your help! > > best wishes, > > Prerona > > >>> On 12 December 2012 11:57, Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu> wrote: >>>> >>>> >>>> 1) Can't hurt to delete. >>>> 2) Yes. >>>> 3) Yes. >>>> >>>> >>>> On Wed, 12 Dec 2012, s0675204 wrote: >>>> >>>>> 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 >>>>> <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
