Freesurfer December 2012

freesurfer@nmr.mgh.harvard.edu

101 participants
161 discussions

Re: [Freesurfer] contrast matrix
by MCLAREN, Donald 11 Dec '12

11 Dec '12

Bo Xiang got the following Error Message. Attached are the mtx and fsgd file. Does anyone what caused the error? > >On Fri, Nov 30, 2012 at 8:28 AM, xiangbo_2010 <xiangbo_2010(a)126.com> wrote: >> Dear Donald McLaren >> >> I used the contrast to run, but the error is appear: >> >> mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd COMTthreeinteryes.fsgd >> dods --C COMTthreeinteryes.mtx --surf fsaverage rh --cortex --glmdir >> lh.COMTthree.glmdir >> >> gdfReadHeader: reading COMTthreeinteryes.fsgd >> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >> Continuous Variable Means (all subjects) >> 0 age 26.2227 11.3891 >> Class Means of each Continuous Variable >> 1 MAC 23.9333 >> 2 MAD 23.5455 >> 3 MAE 24.5000 >> 4 MBC 28.6923 >> 5 MBD 26.3158 >> 6 MBE 30.3750 >> 7 FAC 24.1707 >> 8 FAD 26.4643 >> 9 FAE 25.0909 >> 10 FBC 25.9130 >> 11 FBD 31.5217 >> 12 FBE 34.0000 >> INFO: gd2mtx_method is dods >> Reading source surface /media/freesurfer1/CT/fsaverage/surf/rh.white >> Number of vertices 163842 >> Number of faces 327680 >> Total area 65020.765625 >> AvgVtxArea 0.396850 >> AvgVtxDist 0.717994 >> StdVtxDist 0.193566 >> >> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ >> cwd /media/freesurfer1/CT >> cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd >> COMTthreeinteryes.fsgd dods --C COMTthreeinteryes.mtx --surf fsaverage rh >> --cortex --glmdir lh.COMTthree.glmdir >> sysname Linux >> hostname psylab-desktop >> machine x86_64 >> user psylab >> FixVertexAreaFlag = 1 >> UseMaskWithSmoothing 1 >> OneSampleGroupMean 0 >> y /media/freesurfer1/CT/lh.gender_age.thickness.10.mgh >> logyflag 0 >> usedti 0 >> FSGD COMTthreeinteryes.fsgd >> labelmask /media/freesurfer1/CT/fsaverage/label/rh.cortex.label >> maskinv 0 >> glmdir lh.COMTthree.glmdir >> IllCondOK 0 >> ReScaleX 1 >> DoFFx 0 >> Creating output directory lh.COMTthree.glmdir >> Loading y from /media/freesurfer1/CT/lh.gender_age.thickness.10.mgh >> INFO: gd2mtx_method is dods >> Saving design matrix to lh.COMTthree.glmdir/Xg.dat >> Normalized matrix condition is 82.694 >> Matrix condition is 73313.7 >> Found 149926 points in label. >> Pruning voxels by thr: 0.000000 >> Found 149926 voxels in mask >> Saving mask to lh.COMTthree.glmdir/mask.mgh >> Reshaping mriglm->mask... >> search space = 74490.928733 >> MatrixReadTxT: could not scan value [3][1] >> >> ERROR: loading C COMTthreeinteryes.mtx >> >> thanks! >> >> Bo Xiang >> >> >> >> >> >> At 2012-11-30 06:25:12,"MCLAREN, Donald" <mclaren.donald(a)gmail.com> wrote: >>>Yes. >>> >>>Best Regards, Donald McLaren >>>================= >>>D.G. McLaren, Ph.D. >>>Research Fellow, Department of Neurology, Massachusetts General Hospital >>> and >>>Harvard Medical School >>>Postdoctoral Research Fellow, GRECC, Bedford VA >>>Website: http://www.martinos.org/~mclaren >>>Office: (773) 406-2464 >>>===================== >>>This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >>>HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>>intended only for the use of the individual or entity named above. If the >>>reader of the e-mail is not the intended recipient or the employee or agent >>>responsible for delivering it to the intended recipient, you are hereby >>>notified that you are in possession of confidential and privileged >>>information. Any unauthorized use, disclosure, copying or the taking of any >>>action in reliance on the contents of this information is strictly >>>prohibited and may be unlawful. If you have received this e-mail >>>unintentionally, please immediately notify the sender via telephone at >>> (773) >>>406-2464 or email. >>> >>> >>>On Wed, Nov 28, 2012 at 3:27 AM, xiangbo_2010 <xiangbo_2010(a)126.com> wrote: >>>> Dear Donald McLaren >>>> >>>>>> I want to make interaction between factor 1 (A,B) and factor 2 >>>>>> (C,D,E). >>>>>> age >>>> >>>>>> and gender (M,F) >>>>>> as covariates, I can get 12 classes: ACM ADM AEM BCM BDM BEM ACF ADF >>>>>> AEF >>>>>> BCF BDF BEF and make the contrast: >>>>>> >>>>>> +ACM -ADM 0 -BCM +BDM 0 +ACF -ADF 0 -BCF +BDF 0 age age age age age age >>>>>> age age age age age age >>>>>> 0 +ADM -AEM 0 -BDM +BEM 0 +ADF -AEF 0 -BDF +BEF age age age age age age >>>>>> age age age age age age >>>> because the age and gender as covariates, the column of age should be >>>> instead of 0. the constrast is following: >>>> >>>> 1 -1 0 -1 1 0 1 -1 0 -1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>> 0 1 -1 0 -1 1 0 1 -1 0 -1 1 0 0 0 0 0 0 0 0 0 0 0 0 >>>> is correct? thanks! >>>> >>>> Bo Xiang >>>> >>>> >>>> At 2012-11-22 11:15:08,"MCLAREN, Donald" <mclaren.donald(a)gmail.com> >>>> wrote: >>>>>Please provide us with what each column represents. There seems to be >>>>>too many zeros. >>>>> >>>>>Best Regards, Donald McLaren >>>>>================= >>>>>D.G. McLaren, Ph.D. >>>>>Research Fellow, Department of Neurology, Massachusetts General Hospital >>>>> and >>>>>Harvard Medical School >>>>>Postdoctoral Research Fellow, GRECC, Bedford VA >>>>>Website: http://www.martinos.org/~mclaren >>>>>Office: (773) 406-2464 >>>>>===================== >>>>>This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >>>>>HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>>>>intended only for the use of the individual or entity named above. If the >>>>>reader of the e-mail is not the intended recipient or the employee or >>>>> agent >>>>>responsible for delivering it to the intended recipient, you are hereby >>>>>notified that you are in possession of confidential and privileged >>>>>information. Any unauthorized use, disclosure, copying or the taking of >>>>> any >>>>>action in reliance on the contents of this information is strictly >>>>>prohibited and may be unlawful. If you have received this e-mail >>>>>unintentionally, please immediately notify the sender via telephone at >>>>> (773) >>>>>406-2464 or email. >>>>> >>>>> >>>>>On Wed, Nov 21, 2012 at 7:26 PM, xiangbo_2010 <xiangbo_2010(a)126.com> >>>>> wrote: >>>>>> Dear Donald McLaren >>>>>> >>>>>> I want to make interaction between factor 1 (A,B)and factor 2(C,D,E). >>>>>> age >>>>>> and gender (M,F) >>>>>> as covariates, I can get 12 classes: ACM ADM AEM BCM BDM BEM ACF ADF >>>>>> AEF >>>>>> BCF BDF BEF and make the contrast: >>>>>> >>>>>> +ACM -ADM 0 -BCM +BDM 0 +ACF -ADF 0 -BCF +BDF 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>> 0 +ADM -AEM 0 -BDM +BEM 0 +ADF -AEF 0 -BDF +BEF 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>> 0 >>>>>> >>>>>> is correct? thanks! >>>>>> >>>>>> Bo Xiang >>>>>> >>>>>> >>>>>> At 2012-11-22 08:55:29,"MCLAREN, Donald" <mclaren.donald(a)gmail.com> >>>>>> wrote: >>>>>>>Please explain what are the columns represent. >>>>>>> >>>>>>>Best Regards, Donald McLaren >>>>>>>================= >>>>>>>D.G. McLaren, Ph.D. >>>>>>>Research Fellow, Department of Neurology, Massachusetts General >>>>>>> Hospital >>>>>>> and >>>>>>>Harvard Medical School >>>>>>>Postdoctoral Research Fellow, GRECC, Bedford VA >>>>>>>Website: http://www.martinos.org/~mclaren >>>>>>>Office: (773) 406-2464 >>>>>>>===================== >>>>>>>This e-mail contains CONFIDENTIAL INFORMATION which may contain >>>>>>> PROTECTED >>>>>>>HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>>>>>>intended only for the use of the individual or entity named above. If >>>>>>> the >>>>>>>reader of the e-mail is not the intended recipient or the employee or >>>>>>> agent >>>>>>>responsible for delivering it to the intended recipient, you are hereby >>>>>>>notified that you are in possession of confidential and privileged >>>>>>>information. Any unauthorized use, disclosure, copying or the taking of >>>>>>> any >>>>>>>action in reliance on the contents of this information is strictly >>>>>>>prohibited and may be unlawful. If you have received this e-mail >>>>>>>unintentionally, please immediately notify the sender via telephone at >>>>>>> (773) >>>>>>>406-2464 or email. >>>>>>> >>>>>>> >>>>>>>On Wed, Nov 21, 2012 at 2:50 PM, <xiangbo_2010(a)126.com> wrote: >>>>>>>> No, I want to compute the interaction between factor 1 and factor 2 , >>>>>>>> gender and age as covariates. thanks >>>>>>>> >>>>>>>> Bo Xiang >>>>>>>> >>>>>>>> 在 2012-11-22 04:22:06，"Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> 写道： >>>>>>>>>Hi Bo, I don't understand the contrast you are trying to make. Are >>>>>>>>> you >>>>>>>>>really trying to compute the interaction between four variables >>>>>>>>> (factor >>>>>>>>>1, factor 2, gender, and age)? >>>>>>>>>doug >>>>>>>>> >>>>>>>>>On 11/21/2012 10:49 AM, xiangbo_2010 wrote: >>>>>>>>>> Dear Donald McLaren >>>>>>>>>> Thank you for your reply! I make the contrast according to your >>>>>>>>>> method >>>>>>>>>> is following，but I want to make interaction between factor 1 >>>>>>>>>> (A,B)and >>>>>>>>>> factor 2(C,D,E), gender (M,F) and one continuous variable (age) as >>>>>>>>>> covariates, the following contrast: >>>>>>>>>> 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> 0 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>>>>>>>> is correct? Thanks! >>>>>>>>>> Bo Xiang >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> At 2012-11-21 04:07:37,"MCLAREN, Donald"<mclaren.donald(a)gmail.com >>>>>>>>>> <mailto:mclaren.donald@gmail.com>> wrote: >>>>>>>>>> >On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve >>>>>>>>>> ><greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>>>>>>>>> > wrote: >>>>>>>>>> >> Thanks Donald. Is this the standard way to do this? I had used >>>>>>>>>> >> 8 >>>>>>>>>> >> rows >>>>>>>>>> >> instead of 4 with the difference being that 8 rows gives you an >>>>>>>>>> >> opportunity >>>>>>>>>> >> to look for an effect in males OR females. >>>>>>>>>> > >>>>>>>>>> >Yes. Having 8 rows would tell you if you have an interaction >>>>>>>>>> > between >>>>>>>>>> >factor 1 and 2 in either males or females. My 4 rows only tell you >>>>>>>>>> > if >>>>>>>>>> >the interaction exists. Technically speaking, one would run the >>>>>>>>>> >three-way interaction first. If nothing existed then you do the >>>>>>>>>> >two-way interaction as I suggested. If there is a three-way >>>>>>>>>> >interaction, then you would use Doug's approach of the interaction >>>>>>>>>> > in >>>>>>>>>> >either males or females. >>>>>>>>>> > >>>>>>>>>> >If there is an effect in both >>>>>>>>>> >> males and females but the effects go in opposite directions, >>>>>>>>>> >> then >>>>>>>>>> >> the 4 row >>>>>>>>>> >> implementation will resolve to 0 (no effect). Or am I >>>>>>>>>> >> misunderstanding >>>>>>>>>> >> something (again:)? >>>>>>>>>> > >>>>>>>>>> >Nope. You are right. If the male and female effects are different, >>>>>>>>>> >then they could cancel each other out. If you suspect this to be >>>>>>>>>> > the >>>>>>>>>> >case, then you should be able to demonstrate a three-way >>>>>>>>>> > interaction. >>>>>>>>>> > >>>>>>>>>> >> thanks! >>>>>>>>>> >> doug >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> On 11/20/2012 01:50 PM, MCLAREN, Donald wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Bo, >>>>>>>>>> >>> >>>>>>>>>> >>> Doug asked me to chime in on your issue. Here are some points >>>>>>>>>> >>> that >>>>>>>>>> >>> you >>>>>>>>>> >>> (and others) will hopefully find useful. >>>>>>>>>> >>> >>>>>>>>>> >>> (1) Inferences are two-step process. First, you create and >>>>>>>>>> >>> estimate >>>>>>>>>> >>> the design matrix. Every column in the design matrix accounts >>>>>>>>>> >>> can >>>>>>>>>> >>> account for some of the variance in the data. Second, you have >>>>>>>>>> >>> contrasts that allow you to infer specific effects. Because >>>>>>>>>> >>> the >>>>>>>>>> >>> model >>>>>>>>>> >>> contains your covariates, you are always controlling for the >>>>>>>>>> >>> covariates and by extension any factor/covariate not in the >>>>>>>>>> >>> contrast. >>>>>>>>>> >>> >>>>>>>>>> >>> (2) Forming contrasts is often the most difficult thing to do. >>>>>>>>>> >>> I >>>>>>>>>> >>> assume that your three factors (1, 2, and gender) are all >>>>>>>>>> >>> between-subject factors. If one of them is a within-subject >>>>>>>>>> >>> factor >>>>>>>>>> >>> please let me know and disregard the rest of the email. The >>>>>>>>>> >>> final >>>>>>>>>> >>> F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 >>>>>>>>>> >>> levels >>>>>>>>>> >>> -1)=(3-1)*(3-1)=2*2=4 >>>>>>>>>> >>> >>>>>>>>>> >>> The following is an outline for creating contrasts: >>>>>>>>>> >>> (a) Start simple - difference between levels of 1 factor >>>>>>>>>> >>> (b) Define your null hypothesis: AO=AP=AQ >>>>>>>>>> >>> (c) Make it equal to 0: AO-AP=0 AND AP-AQ=0 >>>>>>>>>> >>> (d) Repeat for the other levels of the factor... >>>>>>>>>> >>> BO-BP=0 AND BP-BQ=0 >>>>>>>>>> >>> CO-CP=0 AND CP-CQ=0 >>>>>>>>>> >>> >>>>>>>>>> >>> (e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ >>>>>>>>>> >>> >>>>>>>>>> >>> (f) Make them equal to 0: >>>>>>>>>> >>> AO-AP-BO+BP=0 >>>>>>>>>> >>> BO-BP-CO+CP=0 >>>>>>>>>> >>> AP-AQ-BP+BQ=0 >>>>>>>>>> >>> BP-BQ-CP+CQ=0 >>>>>>>>>> >>> >>>>>>>>>> >>> (g) Expand them to include gender, for example: >>>>>>>>>> >>> AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0 >>>>>>>>>> >>> >>>>>>>>>> >>> Since the contrast now has 2 columns per level, you should >>>>>>>>>> >>> divide >>>>>>>>>> >>> all >>>>>>>>>> >>> values by 2. This will produce the correct amplitude and >>>>>>>>>> >>> statistics. >>>>>>>>>> >>> If you leave the values as 1 and -1, then you will have an >>>>>>>>>> >>> incorrect >>>>>>>>>> >>> amplitude, but the statistics will still be correct. >>>>>>>>>> >>> >>>>>>>>>> >>> (h) Fill in the respective columns of your design matrix. >>>>>>>>>> >>> >>>>>>>>>> >>> (3) The degrees of freedom are defined based on the rows of >>>>>>>>>> >>> the >>>>>>>>>> >>> F-matrix and the number of rows in the design matrix. The >>>>>>>>>> >>> F-test >>>>>>>>>> >>> has a >>>>>>>>>> >>> numerator and denominator degrees of freedom. F(n,d). >>>>>>>>>> >>> >>>>>>>>>> >>> Best Regards, Donald McLaren >>>>>>>>>> >>> ================= >>>>>>>>>> >>> D.G. McLaren, Ph.D. >>>>>>>>>> >>> Research Fellow, Department of Neurology, Massachusetts >>>>>>>>>> >>> General >>>>>>>>>> >>> Hospital >>>>>>>>>> >>> and >>>>>>>>>> >>> Harvard Medical School >>>>>>>>>> >>> Postdoctoral Research Fellow, GRECC, Bedford VA >>>>>>>>>> >>> Website: http://www.martinos.org/~mclaren >>>>>>>>>> >>> Office: (773) 406-2464 >>>>>>>>>> >>> ===================== >>>>>>>>>> >>> This e-mail contains CONFIDENTIAL INFORMATION which may >>>>>>>>>> >>> contain >>>>>>>>>> >>> PROTECTED >>>>>>>>>> >>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and >>>>>>>>>> >>> which is >>>>>>>>>> >>> intended only for the use of the individual or entity named >>>>>>>>>> >>> above. >>>>>>>>>> >>> If the >>>>>>>>>> >>> reader of the e-mail is not the intended recipient or the >>>>>>>>>> >>> employee >>>>>>>>>> >>> or >>>>>>>>>> >>> agent >>>>>>>>>> >>> responsible for delivering it to the intended recipient, you >>>>>>>>>> >>> are >>>>>>>>>> >>> hereby >>>>>>>>>> >>> notified that you are in possession of confidential and >>>>>>>>>> >>> privileged >>>>>>>>>> >>> information. Any unauthorized use, disclosure, copying or the >>>>>>>>>> >>> taking of >>>>>>>>>> >>> any >>>>>>>>>> >>> action in reliance on the contents of this information is >>>>>>>>>> >>> strictly >>>>>>>>>> >>> prohibited and may be unlawful. If you have received this >>>>>>>>>> >>> e-mail >>>>>>>>>> >>> unintentionally, please immediately notify the sender via >>>>>>>>>> >>> telephone at >>>>>>>>>> >>> (773) >>>>>>>>>> >>> 406-2464 or email. >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Tue, Nov 20, 2012 at 8:17 AM, >>>>>>>>>> >>> xiangbo_2010<xiangbo_2010(a)126.com >>>>>>>>>> >>> <mailto:xiangbo_2010@126.com>> >>>>>>>>>> >>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Dear doug >>>>>>>>>> >>>> Thank you for your reply! >>>>>>>>>> >>>> +AOM -BOM -APM -BPM 0 0 0 0 0 >>>>>>>>>> >>>> +AOM -BOM 0 0 -AQM +BQM 0 0 0 >>>>>>>>>> >>>> +AOM 0 -APM 0 0 0 -COM +CPM 0 >>>>>>>>>> >>>> +AOM 0 0 0 -AQM -COM 0 +CQM >>>>>>>>>> >>>> there should be use 1 -1 or 0.5 -0.5? whether the -BPM should >>>>>>>>>> >>>> be >>>>>>>>>> >>>> change >>>>>>>>>> >>>> BPM? >>>>>>>>>> >>>> Thanks >>>>>>>>>> >>>> >>>>>>>>>> >>>> Bo Xiang >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> At 2012-11-19 07:23:31,"Douglas >>>>>>>>>> >>>> Greve"<greve(a)nmr.mgh.harvard.edu >>>>>>>>>> >>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> Hi Bo, you can think of the Ftest as a logical 'OR' between >>>>>>>>>> >>>> the >>>>>>>>>> >>>> t-test >>>>>>>>>> >>>> contrasts indicated in each row. Each row is a difference of >>>>>>>>>> >>>> differences, >>>>>>>>>> >>>> so >>>>>>>>>> >>>> >>>>>>>>>> >>>> 1. (A-B)om - (A-B)pm --> Does the difference between A and >>>>>>>>>> >>>> B >>>>>>>>>> >>>> differ >>>>>>>>>> >>>> between >>>>>>>>>> >>>> groups O and P for Males? >>>>>>>>>> >>>> 2. (A-B)om - (A-B)qm >>>>>>>>>> >>>> 3. (A-C)om - (A-C)pm >>>>>>>>>> >>>> 4. (A-C)om - (A-C)qm >>>>>>>>>> >>>> 5. (A-B)of - (A-B)pf --> Does the difference between A and >>>>>>>>>> >>>> B >>>>>>>>>> >>>> differ >>>>>>>>>> >>>> between >>>>>>>>>> >>>> groups O and P for Females? >>>>>>>>>> >>>> 6. (A-B)of - (A-B)qf >>>>>>>>>> >>>> 7. (A-C)of - (A-C)pf >>>>>>>>>> >>>> 8. (A-C)of - (A-C)pf >>>>>>>>>> >>>> >>>>>>>>>> >>>> I've put together the first 9 columns of the first 4 rows. >>>>>>>>>> >>>> The >>>>>>>>>> >>>> last 9 >>>>>>>>>> >>>> columns are all 0s. For the last for rows, the 0s and below >>>>>>>>>> >>>> matrix are >>>>>>>>>> >>>> swapped to give you the same for the females >>>>>>>>>> >>>> >>>>>>>>>> >>>> doug >>>>>>>>>> >>>> >>>>>>>>>> >>>> AOM BOM APM BPM AQM BQM COM CPM CQM >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> -------------------------------------------------------------------------- >>>>>>>>>> >>>> +AOM -BOM -APM -BPM 0 0 0 0 0 >>>>>>>>>> >>>> +AOM -BOM 0 0 -AQM +BQM 0 0 0 >>>>>>>>>> >>>> +AOM 0 -APM 0 0 0 -COM +CPM 0&! nbsp;&nb sp; >>>>>>>>>> >>>> >>>>>>>>>> >>>> +AOM 0 0 0 -AQM -COM 0 +CQM >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> On 11/17/12 9:21 PM, xiangbo_2010 wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Hi Freesurfer experts, >>>>>>>>>> >>>> >>>>>>>>>> >>>> I'm very sorry to bother you, but I am very confused with the >>>>>>>>>> >>>> following >>>>>>>>>> >>>> questions: >>>>>>>>>> >>>> >>>>>>>>>> >>>> My experimental design includes three discrete factors: >>>>>>>>>> >>>> factor >>>>>>>>>> >>>> 1 >>>>>>>>>> >>>> with >>>>>>>>>> >>>> three >>>>>>>>>> >>>> levels (A,B,C ); factor 2 with three levels (O,P,Q); gender >>>>>>>>>> >>>> (F, >>>>>>>>>> >>>> M), and >>>>>>>>>> >>>> one >>>>>>>>>> >>>> covariate. >>>>>>>>>> >>>> >>>>>>>>>> >>>> So I can get 18 classes: FAO, >>>>>>>>>> >>>> FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, >>>>>>>>>> >>>> MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the >>>>>>>>>> >>>> interaction >>>>>>>>>> >>>> between >>>>>>>>>> >>>> factor 1 and factor 2 regressing out the effect of gender and >>>>>>>>>> >>>> one >>>>>>>>>> >>>> covariate, >>>>>>>>>> >>>> but I don't know the rules for setting the contrasts for the >>>>>>>>>> >>>> F-test. The >>>>>>>>>> >>>> contrast matrix I used is: >>>>>>>>>> >>>> >>>>>>>>>> >>>> 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> >>>>>>>>>> >>>> 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> >>>>>>>>>> >>>> 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> >>>>>>>>>> >>>> 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> >>>>>>>>>> >>>> 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> >>>>>>>>>> >>>> 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> >>>>>>>>>> >>>> 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> >>>>>>>>>> >>>> 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> 0 0 0 0 >>>>>>>>>> >>>> 0 >>>>>>>>>> >>>> >>>>>>>>>> >>>> is it correct? >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> Any help will be very appreciated. >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> Best wishes, >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> Bo Xiang >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> _______________________________________________ >>>>>>>>>> >>>> Freesurfer mailing list >>>>>>>>>> >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> _______________________________________________ >>>>>>>>>> >>>> Freesurfer mailing list >>>>>>>>>> >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> >>>> <mailto: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. >>>>>>>>>> >>>> >>>>>>>>>> >>> >>>>>>>>>> >> >>>>>>>>>> >> -- >>>>>>>>>> >> Douglas N. Greve, Ph.D. >>>>>>>>>> >> MGH-NMR Center >>>>>>>>>> >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>>> >> Phone Number: 617-724-2358 >>>>>>>>>> >> Fax: 617-726-7422 >>>>>>>>>> >> >>>>>>>>>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> >> Outgoing: >>>>>>>>>> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>>>> >> >>>>>>>>>> >_______________________________________________ >>>>>>>>>> >Freesurfer mailing list >>>>>>>>>> >Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> > <mailto:Freesurfer@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 >>>>>>>>> >>>>>>>>>-- >>>>>>>>>Douglas N. Greve, Ph.D. >>>>>>>>>MGH-NMR Center >>>>>>>>>greve(a)nmr.mgh.harvard.edu >>>>>>>>>Phone Number: 617-724-2358 >>>>>>>>>Fax: 617-726-7422 >>>>>>>>> >>>>>>>>>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>Outgoing: >>>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>>> >>>>>>>>>_______________________________________________ >>>>>>>>>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 >>>>>>> >>>>>>>_______________________________________________ >>>>>>>Freesurfer mailing list >>>>>>>Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >> >> >>

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Re: [Freesurfer] Fwd: Running Tracula: trac-preproc exited with ERRORS
by s0675204 10 Dec '12

10 Dec '12

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

color bar question again
by Longchuan Li 10 Dec '12

10 Dec '12

Hi, FreeSurfer experts I am sorry to bother again, but it seems that my color bar issue is still not solved. I was told last time that the reason for the minimal values in the color bar not properly shown is probably because their values were too small. However, when I display two other overlay files (see attached), I still notice that the minimal values are not properly shown in the color bar either. Is there any function in the overlay display that I am missing to have this mismatched color bar? Many thanks in advance! Longchuan

1 0

Re: [Freesurfer] Longitudinal analysis - contrast
by Alex Hanganu 10 Dec '12

10 Dec '12

Hi Jorge, Thank you very much !! It worked !! I used the new versions: /lme_mass_F1; lms_mass_fit1 /and/lme_mass_fit_vw1/, which you sent me for the old Matlab. Additionally, I uploaded in Matlab - /lme_fit_init; lme_FSfit; lme_Gradient; vec; lme_E1/; /fs_write_fstats; fs_write_Y;/ it ended with: "/Algorithm did not converge at 0 percent/" I suppose this means everything went fine. Total time - 90 minutes. /fstats/ - finished OK /fs_write_stats/ - finished OK. I opened the sig.mgh and the results are ok ! :) Thank you very much for your support Jorge !! Have a great week ! Sincerely, Alex Le 08/12/2012 12:23 PM, jorge luis a écrit : > Hi Alex > > Here is a non-parallel version of the vertex-wise mixed effects models. > You should be able to run it in your old Matlab. > > Just type > > [stats,st] = lme_mass_fit_vw1(X,[1],Y,ni,lhcortex); > > and then the inference: > > CM.C = [0 0 0 1]; > > fstats = lme_mass_F1(stats,CM); > > > Another thing: if you don't see enough signal in your statistical map, > you can smooth the data a bit more eg. FWHM = 15mm. On the other hand, > if you are happy with the amount of signal, then you should keep the > smoothing level at 10mm (so you keep most of the spatial resolution of > the data). > > Best > -Jorge > > > > > > ------------------------------------------------------------------------ > *De:* Alex Hanganu <al.hanganu(a)yahoo.ca> > *Para:* Jorge Luis <jbernal0019(a)yahoo.es> > *Enviado:* Viernes 7 de diciembre de 2012 23:59 > *Asunto:* Re: Re: [Freesurfer] Longitudinal analysis - contrast > > Ok ! > > The good part - you were right - something changed - the error :) > > Now its: > /??? Undefined function or method 'matlabpool' for input arguments ... > Error in lme_mass_fit at 123 > Error in ==> lme_mass_fit_vw at 73 > / > I will try this again on Monday, on the mac of my colleague, who > has a newer version of Matlab. > > Thanks for helping at such a late hour ! > > Have a nice evening , > > Sincerely, > > Alex. > > > > > Le 07/12/2012 11:33 PM, jorge luis a écrit : >> Hi Alex >> >> I've just discovered what is the problem that you are >> experiencing. Your version of Matlab is too old and it is not >> very friendly with variables within a parfor loop statement as >> newer Matlab versions are. You have either of two choices: >> >> 1- Update your Matlab to a 2011 or later version (lme will run >> very fast). >> 2- Go into lme_mass_fit function and change the parfor statement >> by a simple for loop (everywhere in the code where you see the >> word "parfor" change it by the word "for") and run your analyses >> with a single processor: >> >> stats = lme_mass_fit_vw(X,1,Y,ni,lhcortex,[],1); >> >> the analysis is going to be slower but you will have the job done. >> >> You will have to do the same with every parallel function that >> you are going to use. For example you are going to use: >> >> CM.C = [0 0 0 1]; >> fstats = lme_mass_F(stats,CM,1); >> >> for the inference step. Thus, you will have to change every >> "parfor" in lme_mass_F by a simple "for". >> >> Hope this will solve your problem. >> Best >> -Jorge >>

1 0

which step comes first
by Catherine Bois 10 Dec '12

10 Dec '12

Hi, when reconstructing the brains including manual edits, does the step that incorporates control points "come before" the white matter edits? Ie so if I do both control points and white matter edits, will the white matter edits be take into account even if I just use -autorecon -cp , and not -wm? Thanks

3 2

nuisance variable ICV
by Berg, S.F. van den 10 Dec '12

10 Dec '12

Hi Freesurfer Experts, Just to make it sure i have a question about correcting for cranial size. I compared two groups, 100 patients versus 50 Controls. I entered a discrete variable 'groups' (Patients: 1 and controls:2) in qdec. For cortical thickness difference between these groups, do i have to control for total intracranial volume? ICV (intra cranial volume is output from aseg2tables) or controlling for another variable which estimate total brain volume, like total gray matter or supra tentorial volume? In my correlation analyses, relating cognitive peformance and cortical thickness within the patient group. Do i have to control for ICV or Total gray matter? besides the variable age, gender and education. I think only volume differences between groups need controlling for ICV, is that correct? And in my correlation analyses, relating cognitive performance ato subcortical volume within the patient group. Do i have to control for ICV or Total gray matter? besides the variables age, gender and education. Do you have a reference to a methodological paper, which descibes different (anatomical) nuisance factors and their influence on the data? Is there a automated correction for brain size in the cortical and subcortical freesurfer stream (step of recon -all command)? Many Thanks, Stan

3 2

Re: [Freesurfer] abblocked documentation?
by Douglas N Greve 10 Dec '12

10 Dec '12

Hi Summer, there is some documentation in mkanalysis-sess -help. It's not very much documentation, so I just wrote a little bit more which I have included below. Let me know if you still have questions. doug -abblocked PeriodSec Design is AB-Blocked (ie, periodic, two condition). Specify the period of stimuluation in seconds (NOTE: in previous versions you had to specify the number of cycles). No paradigm file is required. When selxavg3-sess is run, it will automatically create a Fourier analysis with components at the fundamental and first harmonic as well as components at a frequency just below and above the fundamental for a total of 4 frequencies each of which will have a real and imaginary component for a total of 8 regressors. It will also create a contrast called "fund" (for "fundamental"). This contrast will be a F-contrast to test both the real (cosine) and imaginary (sine) components of the fundamental frequency with the fsig volume being the final result. There will also be other files there including real.nii and imag.nii which are the real and imaginary components. There will also be angle.nii and angle.masked.nii which will be the angle between the real and imaginary; the masked version will be masked by fsig > 2. On 12/06/2012 07:38 PM, Summer Sheremata wrote: > Hi Doug, > > Could you point me to the documentation for abblocked designs in freesurfer 5. I'm having trouble figuring out the analysis. > > Thank you, > > Summer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

R: Re: convert size
by Andrea Tateo 10 Dec '12

10 Dec '12

Soory if I bother you again, actually I would like to convert from 256,128,256 to 256,256,256 and from 181,145,181 to 256,256,256. Can you tell me the complete command and not just the option. thanks immensely Andrea ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 10-dic-2012 14.36 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] convert size Hi Andrea I think there is a typo in your email as your sizes are the same. If you have a volume you would like to reslice it like you can use the -rl <volume> option to do what you want. cheers Bruce On Mon, 10 Dec 2012, Andrea Tateo wrote: > Hello FS experts, > I would like to to convert binary images from size 256,256,256 voxels to > size 256, 256, 256. > > Is there any FreeSurfer's module to make it? > > Thank you very much > > Andrea > > 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

Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 10 Dec '12

10 Dec '12

Hi Julia, that command is fine. It will not use the fieldsign or eccen. doug On 12/10/2012 10:17 AM, Julia Foecker wrote: > Dear Doug, > > I tried version 5 with the commands suggested on the webside and this is > working > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) > > > However, I have only polar angle runs and I am not sure if the rtview commands > is only referring to polar angle maps (because the field signs are included and > I think that they consist of eccentricity maps as well which do not have a > meaning in my analysis). > How do I have to change the command below so that it is just referring to polar > maps? > > rtview --s VGP01 --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz > --fsig polar/fsig.nii.gz > > > Many thanks for further suggestions, > Julia > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

Detrending timeseries with yhat.mgh from mri_glmfit
by Chris McNorgan 10 Dec '12

10 Dec '12

Hello, I have a question regarding the yhat.mgh file generated from some resting-state functional data after running: mri_glmfit --y fmcpr.siemens.sm0.self.?h.nii.gz --glmdir $dest_dirname --qa --save-yhat I had assumed that the yhat file was the detrended data, but after plotting it in matlab and seeing perfectly smooth lines, I came to believe that the yhat.mgh file represents the trendline for each timeseries in the source .nii.gz? In this case, if I use mri_segstats to pull out the timeseries data from an ROI, is it then valid to calculate roi_timeseries/roi_trendline in order to arrive at a detrended timeseries for that ROI? Thanks, Chris

2 1

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Freesurfer December 2012