Freesurfer December 2012

freesurfer@nmr.mgh.harvard.edu

101 participants
161 discussions

tracula - posterior density just one-dimensional curve
by Andi Heckel 20 Dec '12

20 Dec '12

Dear Tracula team, I have noticed in a multisubject tracula analysis, that the posterior density in many if not all paths in the path.pd.nii.gz file is just a bright one-dimensional curve, rather than a true distribution. The path.map.nii.gz is empty. This is true for both flirt and bbreg registered versions in many subjects. Trac-all finished wiithout errors. So did Recon-all. Could it actually be a memory (RAM) problem ? We are running tracula on a cluster with only 2.5 GB per core. thx for any help and kind regards, andi

3 4

trouble with tracula preprocessing step
by s0675204 20 Dec '12

20 Dec '12

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 <s0675204(a)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 >>> <ayendiki(a)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 >>>>> <ayendiki(a)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(a)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(a)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(a)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(a)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(a)sms.ed.ac.uk> >>>>>>>>>>>>>>> Date: 7 December 2012 19:44 >>>>>>>>>>>>>>> Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited >>>>>>>>>>>>>>> with >>>>>>>>>>>>>>> ERRORS >>>>>>>>>>>>>>> To: freesurfer(a)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(a)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(a)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(a)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(a)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. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >>

2 1

Fwd: tracula problem:poor forceps major tract
by bryon mueller 20 Dec '12

20 Dec '12

After processing dozens of subjects through tracula I have found some subjects with tracts that are one voxel along the entire tract, for example the forceps major. After reviewing the data I believe the bvecs files are pointing the correct direction, I believe the registration between the T1/freesurfer segmentation and DTI is reasonably good (registration was performed with bbr), at least the anat_brain_mask-vent.bbr and dtifit_FA are reasonable and cortex.bbr and lowb_brain seem reasonably well registered. The brain extraction does look poor in that a large chunk of posterior skull remains in the anat_brain_mask-vent.bbr image but the as the registrations, segmentations and parcellations look OK I believe this isn't the cause of my problems. I do see one issue: the registration between the dtifit_FA.bbr and fmajor_PP_avg33_mni_bbr_logprior_0 images. Sections of the logprior volume are entirely in the lateral ventricles of the DTI data. Please see attached jpg. This subject large lateral ventricles and I am wondering if such subjects can be run successfully in tracula. Much thanks for any suggestions.

2 2

Monte Carlo
by Susan Alice McLaughlin 20 Dec '12

20 Dec '12

Hi Doug, I am trying to run a Monte Carlo simulation on functional data constrained to a label. Looking at a previous post - https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290… - I see that your advice is to 1) constrain when running mri_glmfit, then 2) use mri_glmfit-sim rather than running mri_glmfit with the simulation options. I have done step 1, however when I try to mri_glmfit-sim, I receive a "command not found" message. I confess that I am running an old version of Freesurfer (v 1.133.2.5). Is this my problem? If so, will it be a problem if I run mri_glmfit with the simulation options? Thank you and happy holidays, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

1 0

downloading GradientUnwarping
by John Drozd 20 Dec '12

20 Dec '12

Hello, I would like to download and install the software described at http://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping Your email address is listed on this website. I cannot find a download link. We would like to use this with Freesurfer. Do you know where I can download this software from? Thank you, John John J. Drozd, M.Sc., Ph.D. Post-Doctoral Fellow Robarts Research Institute Western University London, Ontario, Canada

2 2

Re: [Freesurfer] Error with fs-fast selxavg3-sess
by Yuval Harpaz 20 Dec '12

20 Dec '12

> Dear FreeSurfer group > I am new to free surfer and have dificulties running fs-fast analysis for > the first time > I use freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu but ran > the same commands for the same data on a NMR computer (nmr-stable5.0-env) > which gave the same error > the data was acquired using GE machine > > I have 1 subject 2 conditions and used the below commands to process my > data > running selxavg3-sess gave errors for gammafit and FIR. here is the > script and error for gammafit. > > mkanalysis-sess -analysis vg.sm5.lh -surface self lh -event-related > -paradigm VG.par -polyfit 2 -nskip 0 -nconditions 2 -TR 4 -mcextreg -fsd > bold -gammafit 2.25 1.25 -fwhm 5 -refeventdur 3 > mkcontrast-sess -analysis vg.sm5.lh -contrast VG-vs-OE -a 2 -c 1 > selxavg3-sess -s vgoe -analysis vg.sm5.lh > ... > Output argument "partype" (and maybe others) not assigned during call to > > "/usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_ldpar4.m>fast_ldpar4". > > Error in flac_customize (line 123) > [par partype] = fast_ldpar4(parpath); > > Error in fast_selxavg3 (line 67) > flac0 = flac_customize(flac0); > > > for FIR the error was > > ERROR: creating FIR design matrix for Condition01 > ??? Attempt to reference field of non-structure array. > > Error in ==> flac_customize at 357 > if(~isempty(flacnew.TFmtx)) > > Error in ==> fast_selxavg3 at 65 > flac0 = flac_customize(flac0); > > do you have any idea what it might be? > at some point I got complaints about NaNs in my data which are not allowed > for SVD but I cannot replicate the error > thanks > -- > Yuval > > > > > Dr .Harpaz > > BIU MEG lab <http://faculty.biu.ac.il/~goldsa/index.html> >

2 1

Running SPM8
by Staples, Lindsay Katharine 20 Dec '12

20 Dec '12

Hi- Our Unix system was recently updated and I am now unable to use SPM 8 from /autofs/space/grover_001 or from /autofs/space/bert_002. I get the following message: Initialising SPM...Error using fileparts Too many output arguments. Error in cfg_util>local_initapps (line 1217) [p n e v] = fileparts(appcfgs{k}); Error in cfg_util (line 587) local_initapps; Error in spm_jobman (line 149) cfg_util('initcfg'); % This must be the first call to cfg_util Error in spm (line 344) spm_jobman('initcfg'); Any words of wisdom? Thanks! Lindsay

1 0

putamen seg
by Gregory Kirk 20 Dec '12

20 Dec '12

Hi, tried to use control points to improve the segmentation of the putamen in the difficult area between putamen,claustrum & insula. adding some white matter control points does not seem to insluence the aseg segmentation. control points are set to 110 after reprocessing with recon-all -autorecon2-cp -autorecon3 -subjid 008 ( v5.1), but these same points are still labeled as putamen? also i do see that some white matter filaments have leaked into the putamen, so the mailing list comments that control points would mess it up seems it would be correct ( if it was affecting the putamen seg, which it does not seem to have done at all). so options are manual editing, here ask opinions, the extra tissue added between the putamen&insula it is doing consistently, so taking the unedited volumes, after checking there are no odd other things added or missing might be more unbiased estimate, that volumes after several human raters had selectively removed a few voxels here and there ? any opinions ? thanks greg

2 1

Re: [Freesurfer] space of T1.mgz
by Mojdeh Zamyadi 20 Dec '12

20 Dec '12

Hi there, Sorry, if my question is confusing. This is what I want to do, I have two groups of controls and patients and I've already run recon-all on them. I now want to know the head/body/tail volumes. What I did was: 1. used "mri_binarize" to get the right and left hippocampal masks from the cortical segmentation (using label numbers 17, 53) 2. used "mri_convert" to convert left_hippo.mgz, right_hippo.mgz and T1.mgz into .nii files. 3. use itk SNAP to manually segment the total hippocampus (the freesurfer mask) into head, body and tail. now, my questions is regarding the last step. If the individual segmentations are in the native space, I can't be sure that the landmarks I'm using for head/body/tail separation is always the same (since some of the subjects might be in an oblique space). So would you recommend that I first register the T1 and segmentations all into a common space? Also, I was wondering if the segmentation is going to effect the actual volume (since the brain is going to be stretched and transformed while doing the registration). I hope I made my question clear and I would greatly appreciate your advice. Thanks, -Mojdeh On 12/18/2012 12:58 PM, Bruce Fischl wrote: > Hi Mojdeh > > they are not in atlas space and the volumes are for that subject, so > you shouldn't have to do anything if I understand you correctly > > cheers > Bruce > > On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote: > >> Hi Doug, >> >> Thanks for the quick reply. I actually saw this link before first >> posting my question but it doesn't quite answer my question. What I want >> to know is whether the T1.mgz& aseg.mgz files are in an atlas space? if >> that's the case, it means the segmentation for all my subjects are in >> the same space and I don't need to convert anything if I want to compare >> their hippocampal volumes. I'm not quite sure if any sort of >> registration to an atlas is done in any steps of recon-all or not. I >> would appreciate if could clarify this for me. >> >> Thanks, >> -Mojdeh >> >> On 12/18/2012 12:18 PM, Douglas N Greve wrote: >>> Hi Mojdeh, try looking at this doc >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>> doug >>> >>> On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote: >>>> Hi all, >>>> >>>> I want to segment the hippocampus into head/body/tail in itk SNAP >>>> using >>>> the hippocampus mask that I create from the result of recon-all >>>> segmentation. My question is, are the T1.mgz and aseg.mgz files in the >>>> native space of the image or in the atlas space? I know the voxel size >>>> is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45), >>>> but I want to know if the original images are registered to a common >>>> atlas space or just resampled to a different voxel size. The reason >>>> I'm >>>> asking this, is because I'm doing a group study and I want to make >>>> sure >>>> all my subjects are in the same space so that the segmentation I do is >>>> accurate for all. >>>> >>>> Thanks for your help, >>>> >>>> Mojdeh Zamyadi, MSc >>>> Clinical Research Project Assistant >>>> The Hospital for Sick Children >>>> 555 University Avenue >>>> Toronto ON M5G 1X8 >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. >

2 1

new atlas
by Gabriel Gonzalez Escamilla 20 Dec '12

20 Dec '12

2 1

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Freesurfer December 2012