 |
 |
thanks Mark, ill see the errors and rectify them, thanks a ton have a great week end ahead Regards Hsekar On Fri, Apr 25, 2014 at 4:17 PM, Mark Jenkinson < [log in to unmask]> wrote: > Hi, > > The problem is right at the beginning of your analysis. > Your registrations have failed. > It is really important to go through the process of checking (i.e. looking > at) your outputs, as the wiki page and the FSL Course practical both > explain, before proceeding to the later steps. > > I suspect that your registration is having problems because of the large > amount of neck and initial orientation of your images. This can probably > be solved by running fslreorient2std and robustfov on your images before > doing any of the steps for FIRST. So try that and hopefully it will fix > your problems, but remember to always look at your data and the outputs > from each analysis step. > > All the best, > Mark > > > > > On 25 Apr 2014, at 11:41, R B <[log in to unmask]> > wrote: > > Dear Mark, > I have attached all the files as suggested, do i have to attach the .bvars > &.vtk files of other subcortical structures too. kindly let me know about > it. > i did check the specified folder i found these .bmv files to be precise, i > have BrStem_bin, L_Accu_bin, L_Amyg_bin, L_caud_bin, L_Hipp_bin, > L_Late_bin, R_Accu_bin, R_Amyg_bin, R_Caud_bin, R_Hip_bin, R_Late_bin > thanks in advance for your valuable support > Regards > > Hsekar > > > On Fri, Apr 25, 2014 at 4:01 PM, Mark Jenkinson < > [log in to unmask]> wrote: > >> Hi, >> >> I need to see all the output of run_first_all from one subject, not >> just the bvars file. >> So please send me the vtk and the nifti (nii.gz) files as well. >> >> Also, since I now realise that you are running on Ubuntu, can you check >> that the directory $FSLDIR/data/first/models_336_bin/ contains many .bmv >> files and three directories. I'm asking about this because sometimes on >> Ubuntu systems people can fail to install all the necessary files necessary >> for FIRST to run. >> >> All the best, >> Mark >> >> >> On 25 Apr 2014, at 11:18, R B <[log in to unmask]> wrote: >> >> Dear Mark, >> i have uploaded the files at the specified link, >> output of the run_first_all : FIRST_C_1-L_Hipp_first.bvars >> output after concatenating the bvar files is : L_Hipp_all.bvars >> design matrix: design.mat >> kindly provide ur guidance in proceeding. >> on trying "--useReconMNI" i get the error message >> >> read model >> done reading model >> setting up shape/appearance model >> The shape has 732 vertices. >> 336 modes of variation are retained. >> The model was constructed from 336 training subjects. >> model loaded >> terminate called after throwing an instance of >> 'NEWMAT::ConvergenceException' >> >> but the fsl closes unexpectedly, with the error message, i have >> attached the photoshoot of error message. >> >> thank you >> >> >> On Fri, Apr 25, 2014 at 3:10 PM, Mark Jenkinson < >> [log in to unmask]> wrote: >> >>> Hi, >>> >>> This sounds fine, although something is clearly going wrong given the >>> huge values in your output (e.g. 2.0072e+17 = 2.0072*10^17). I assume that >>> you have checked that the outputs from run_first_all look OK, and that you >>> have created the shape_analysis directory (for your outputs). If so, then >>> I think we need to see some files to understand what is going wrong. Send >>> us the following (single subject output from run_first_all, the output of >>> cancat_bvars and the design.mat). You can send the files to the following >>> site: >>> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C >>> >>> Also, it might be worth trying an analysis with --useReconMNI rather >>> than --useReconNative and --useRigidAlign, just in case there is a problem >>> with the content or location of the individual registration matrices. >>> >>> All the best, >>> Mark >>> >>> >>> On 25 Apr 2014, at 10:31, R B <[log in to unmask]> >>> wrote: >>> >>> Thank U Mark for replying >>> here goes the commands that i have used >>> run_first_all -i Con_01 -o First_Con_01, similarly i did for Con_02, >>> Con_03, Pat_01, Pat_02, Pat_03, >>> so i had files First_Con_01_*.bvars files >>> since i was interested in shape analysis of hippocampus >>> i used concat_bvars FIRST_L_Hippo_all First_Con_01_L_Hipp_first.bvars >>> .........Con_02......... >>> so i had the concatenated file FIRST_L_Hippo_all.bvars >>> i created a design.mat fle, it was just a 2 group design >>> and then i did the command first_utils >>> first_utils --vertexAnalysis --usebvars -i FIRST_L_Hippo_all.bvars -d >>> design.mat -o shape_analysis/con1_dis2_L_Hipp --useReconNative --useRigidAlign -v >& shape_analysis/C_P_L_Hipp_output.txt >>> all these analysis were analysed in the same computer, in the last 3-4 >>> days. and i get the error message. >>> as described earlier >>> >>> thank u in advance for your valuable support >>> >>> regards >>> >>> Hsekar >>> >>> >>> On Fri, Apr 25, 2014 at 2:06 PM, Mark Jenkinson < >>> [log in to unmask]> wrote: >>> >>>> Hi, >>>> >>>> What is the exact command that you are running? >>>> And have you run all the preceding steps yourself recently? >>>> >>>> All the best, >>>> Mark >>>> >>>> >>>> On 24 Apr 2014, at 11:55, R B <[log in to unmask]> wrote: >>>> >>>> Dear Bergsland, >>>> thanks a ton, >>>> i had stuck at this place for weeks, >>>> but in the next step of first_utils >>>> i was shown this error message >>>> >>>> read model >>>> done reading model >>>> setting up shape/appearance model >>>> The shape has 732 vertices. >>>> 336 modes of variation are retained. >>>> The model was constructed from 336 training subjects. >>>> model loaded >>>> read model >>>> done reading model >>>> setting up shape/appearance model >>>> The shape has 732 vertices. >>>> 336 modes of variation are retained. >>>> The model was constructed from 336 training subjects. >>>> 2.0072e+17 881.051 5.25073e-05 0.000188217 >>>> 48.5903 6.41596e-10 2.23193e+17 1.556e+17 >>>> 2.34483e+17 14093.8 2.32187e+17 0.0125242 >>>> 2.0072e+17 14092.6 38.0579 48.5899 >>>> 14096.8 5.25072e-05 13.7711 48.59 >>>> 55.0677 48.59 0.0124105 789.439 >>>> 48.5899 2.00702e+17 2.24266e+17 3.67338e-29 >>>> 194.36 2.44923e+38 55.0588 3.82395e+17 >>>> 12.1476 1.99576e+17 0.00340571 4.8715e+13 >>>> 2.22094e+17 1.9495e+26 2.20981e+17 13.7662 >>>> 1.84873e+17 2.31096e+17 220.208 48.59 >>>> 5.46824e+16 0.00074484 13.7687 2.64842e+17 >>>> 3173.77 1.52252e+17 55.0559 48.5901 >>>> 1.82875e-07 55.058 5.25668e-05 9.38417e+18 >>>> 2.00702e+17 1.68046e+17 14096.8 7.31122e+11 >>>> 4.72724e-05 0.0108808 2.22055e+17 2.51367e+17 >>>> 2.19842e+17 0.0124627 2.11688e+17 220.259 >>>> 12.3975 194.361 -2.18716e+17 3523.67 >>>> 2.81376e-09 -7.65347e+25 0.000225766 55.0587 >>>> -0.00599172 4.19081e-17 3.47812e-07 48.59 >>>> 13.764 5.25678e-05 48.59 2.07462e+17 >>>> 5.2498e-05 2.83983e+17 2.09722e+17 2.08583e+17 >>>> 2.17511e+17 5.43975e+16 880.925 1.54597e+17 >>>> 2.82892e+17 5.2497e-05 5.25064e-05 781.441 >>>> 0.0210916 2.4462e-15 220.235 3526.14 >>>> 48.5901 0.023384 4.52531e-08 2.67103e+17 >>>> 881.02 0.000210025 1.51091e+17 1.14264e+10 >>>> 1.99572e+17 55.0657 2.9558e-06 5.25075e-05 >>>> 46136.4 2.08544e+17 220.259 13.774 >>>> -0.00156579 55.0581 0.00017582 12.1475 >>>> 0.000209969 12.1475 2.33655e+26 12.1475 >>>> 2.28876e+17 5.87024e-19 48.5903 12.1476 >>>> done recon >>>> terminate called after throwing an instance of >>>> 'NEWMAT::ConvergenceException' >>>> >>>> can you pl. guide me what could have possibly gone wrong this error >>>> messae >>>> >>>> >>>> On Thu, Apr 24, 2014 at 1:16 PM, Niels Bergsland <[log in to unmask]>wrote: >>>> >>>>> What output do you get when you run head -n3 on the file generated >>>>> by concat_bvars ? >>>>> >>>>> >>>>> Also, are you really seeing "usr/share/fsl/5.0" rather than >>>>> "/usr/share/fsl/5.0" ? >>>>> >>>>> >>>>> On Thu, Apr 24, 2014 at 9:28 AM, R B <[log in to unmask]> wrote: >>>>> >>>>>> Dear Bergsland >>>>>> Thanks for your reply, >>>>>> so if my understand is correct, after running the command >>>>>> run_first_all on individual subjects i get the .bvars file for each of the >>>>>> subcortical structures. >>>>>> now as i am interested in the shape analysis of left hippocampus, >>>>>> do i have to edit the file " subj01_L_hippo_first.bvars " >>>>>> in that case i the path mentioned in this file is usr/share/fsl/5.0. >>>>>> >>>>>> or did you mention the bvars file generated after the command >>>>>> concat_bvars >>>>>> in this case there is no mention about the destination >>>>>> "usr/share/fsl/5.0" >>>>>> >>>>>> can u kindly please tell me whether i have mis-understood at any >>>>>> step >>>>>> thanks in advance >>>>>> >>>>>> regards >>>>>> >>>>>> hsekar >>>>>> >>>>>> >>>>>> On Wed, Apr 23, 2014 at 7:30 PM, Niels Bergsland < >>>>>> [log in to unmask]> wrote: >>>>>> >>>>>>> The bvars is created when you run FIRST. So you'll find them in the >>>>>>> same directory as your other outputs. >>>>>>> >>>>>>> >>>>>>> On Wed, Apr 23, 2014 at 3:30 PM, Hsekar B <[log in to unmask]>wrote: >>>>>>> >>>>>>>> dear fsl experts >>>>>>>> while performing FSL- FIRST analysis i encountered this problem >>>>>>>> after completing the first_run_all and concat_bvars commands >>>>>>>> i was able to get through these steps without any trouble and >>>>>>>> obtained the output as described in the manual. >>>>>>>> however on initiating the command first_utilis i get the following >>>>>>>> error message. >>>>>>>> >>>>>>>> Warning: does not exist. Attempting to switch to: >>>>>>>> /usr/share/fsl/5.0 >>>>>>>> read model >>>>>>>> Not a vtk file (error in line 1). >>>>>>>> Not a vtk file (error in line 1). >>>>>>>> >>>>>>>> in a link (below) it has been discussed to >>>>>>>> Load the bvar file in a text editor and change anything that looks >>>>>>>> like /usr/local/fsl with the path for your own installation of FSL (which >>>>>>>> might not be /usr/share/fsl/5.0). >>>>>>>> >>>>>>>> >>>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1308&L=fsl&D=0&P=381683 >>>>>>>> >>>>>>>> can anyone kindly let me know where can i get this bvar file, >>>>>>>> >>>>>>>> thanks in advance >>>>>>>> >>>>>>>> regards >>>>>>>> >>>>>>>> RB >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Niels Bergsland >>>>>>> Integration Director >>>>>>> Buffalo Neuroimaging Analysis Center >>>>>>> 100 High St. Buffalo NY 14203 >>>>>>> [log in to unmask] >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Niels Bergsland >>>>> Integration Director >>>>> Buffalo Neuroimaging Analysis Center >>>>> 100 High St. Buffalo NY 14203 >>>>> [log in to unmask] >>>>> >>>> >>>> <C_P_L_Hipp_output.txt> >>>> >>>> >>>> >>> >>> >> >> > >