FIX: Fsl Bedpostx Error

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    Here are some simple methods to help you fix the bedpostx fsl error issue.

    Object:

    Re: Bedpostx Error

    From:

    Stamatios Sotiropoulos <[login to remove mask]>

    Reply:

    fsl bedpostx error

    FSL – FMRIB Software Library <[Enter nowrap>
    fsl bedpostx error

    Date:

    Sat, May 15, New Years Day, 11:08:35 AM Nowrap>

    Content Type:

    constituent / alternative

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    When I do BedpostX FSL preprocessing, I get the following message:

      ----- Bedpostx Monitor -----1 disk processed 622 disks processed by 62.........59 discs processed 6260 associated with processed slices out of 62An error has occurred. Please check the file /Users/...../bedpostx.bedpostX/logs/bpx_postproc.e68944/Users/..../bedpostx.bedpostX/monitor: bond 15: kill: (9187) - No processexit[Process completed] 

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  •   Error in log file: * File "/ Applications / FSL / bin / imglob" line 78    offline "Usage: $ 0 [-extension / extensions] "                     ^SyntaxError: missing square brackets when calling print File "/ Applications / FSL / bin / imglob" line 78    use "Usage: $ 0 [-extension / extensions] "                                      ^SyntaxError: parentheses missing due to call to print File "/ Applications / FSL / bin / imglob" line 78    design "Usage: $ 0 [-extension / extensions] "                               ^SyntaxError: parentheses missing in call to help you "print" Folder "/ Applications / FSL / bin / imglob", title page 7eight    print "Usage: $ 0 [-extension / extensions] "                              ^SyntaxError: missing parentheses when calling print * 

    But I don’t know exactly what that means. This is really weird because the development was almost complete (stopped at It 61 above). I have all the outputs. So my questions might be like this:

    1. What does the error mean?
    2. Is the process not finished yet? (see above, as a rule, it is said)
    3. If not, what can I do to resolve this issue?

    #! / bin / bashCopyright (C) 2004, Oxford Associated University## SHCOPYRIGHTexport LD_LIBRARY_PATH = $ LD_LIBRARY_PATH: $ FSLDIR / libUse() Echo “” Echo “Usage: bedpostx [options]” Echo “” Echo “expects to find bval and bvecs in the material directory” Echo “expected in search data and nodif_brain_mask in topic directory” Echo “expects grad_dev to be in ideas directory if -g is given” Echo “” Echo “:” #echo “-QSYS (queuing system, 0 comes with fsl_sub: FMRIB, 1 PAIR (standard): WashU)” Echo “-Q (name associated with GPU queue, go to standard cuda.q (defined in environment variable: FSLGECUDAQ) ” #echo “-Q (name because of GPU queue, default cuda.q QSYS = 0 and no queue for QSYS = 1)” echo “-NJOBS (count of all jobs in the queue, resources split into NJOBS chunks, useful for GPU cluster, workaround 4)” echo “-n (the number most commonly associated with fibers per voxel is late 3)” echo “-w (ARD weight, more weight means less extra fibers per voxel, default 1)” echo “-b (fade over time, standard 1000)” represent “-j (number of jumps, overdue 1250)” echo (example “-s all, default 25)” specify “model (deconvolution model. 1: and sticks, 2: with incredible scattered sticks (standard), 3: with zeppelins)” Mirror “-g (take into account gradient nonlinearities, standard off)” Echo “” Echo “” Mirror “ALTERNATIVE: You can directly access bedpostx via xfibre options” echo “Just in case: bedpostx –noard –cnonlinear” echo “Enter ‘xfibers –help’ for a list of available options” “The standard options are presented as the Bedpostx standard (see above) and not as the xfibers standard.” introduce “” replicate “Note: use old OR better intax ”. Exit 1monitor () grep “$$ b”make_absolute () dir = $ 1; if [-d $ dir]; thenOLDWD = `pwd`cd $ dirdir_all = `pwd`cd $ OLDWD differentdir_all = $ dir Fi echo $ dir_all[“$ 1” matches “”] && usesubjdir = `make_absolute $ 1`subjdir = `echo $ subjdir | sed ‘s / / $ / $ / g’ ‘echo “———————————————— ——– “echo “———— Bedpostx GPU version ————“echo “———————————————— ——– “echo subjectdir will be $ subjdir# parsing option argumentsqsys = 0njobs = 4n fibers = 3Fondant = 1Burnout = 1000n jumps = 1250Total samples = 25Model = 2gflag = 0other = “”Queue = “”lying downbye [ ! -z. “$ 1”]Do The “1 dollar” case -QSYS) qsys = $ 2; shift ;; -Q) queue = “- q $ 2”; shift ;; -NJOBS) njobs = $ 2; -n) nfibers = $ 2; shift ;; -w) fudge = $ 2; -b) burnin = 2 $; shift ;; -j) njumps = $ 2; shift ;; -s) sampleevery = $ 2; shift ;; -model) model = 2 $; clearance ;; -g) gdrap = 1 ;; *) other = $ other “” $ 1 ;; esac lying downFinishedopts = “- nf = $ nfibers –fudge = $ fudge –bi = $ burnin –nj = $ njumps –se = $ sampleevery –model = $ model”defopts = “- cnonlinear”opts = “$ opts $ defopts $ other”if [$ qsys -eq two] && [“x $ SGE_ROOT”! = “x”]; thenQueue = “- q $ FSLGECUDAQ”Fi# make sure you have all the required written documentsif [ ! -d $ subjdir]; thenecho “Directory object $ 1 instead of found”Exit 1Fiif [ !-e $ subjdir / bvecs]; then if possible [-e $ subjdir / bvecs.txt]; thenmv $ subjdir / bvecs.txt $ subjdir / bvecs differentecho “$ subjdir / bvecs not only found”Exit 1 FiFiif [ ! -e $ subjdir / bval]; then if -e [$ subjdir / bval.txt]; thenmv $ subjdir / bval.txt $ subjdir / bval differentecho “$ subjdir / bval as opposed to found”Exit 1 FiFiif [`$ FSLDIR / bin / imtest $ subjdir / data` -eq 0]; thenecho “$ subjdir / data not found”Exit 1Fiif [$ gflag -eq 1]; then if [`$ FSLDIR / bin / imtest $ subjdir / grad_dev` -eq]; thenecho “$ subjdir / grad_dev is not considered found”Exit 1 FiFiif [`$ FSLDIR / bin / imtest $ subjdir / nodif_brain_mask` -eq 0]; thenecho “$ subjdir / nodif_brain_mask not found”Exit 1Fiif [-orite $ subjdir.bedpostX / xfms / eye.mat]; thenecho “$ subjdir being processed: was $ subjdir.bedpostX.”echo “Please remove or possibly rename $ subjdir.bedpostX before trying again.”Exit 1FiCreate echo Bedpostx directory structuremkdir -r $ subjdir.bedpostX /mkdir -p $ subjdir.bedpostX / diff_partsmkdir -p $ subjdir.bedpostX / logsmkdir -significant $ subjdir.bedpostX / logs / logs_gpumkdir -p $ subjdir.bedpostX / logs / monitorrm -f $ subjdir.bedpostX / logs / monitor / *mkdir -p $ subjdir.bedpostX / xfms#mailto=`whoami`@fmrib.ox.ac.Copying ukecho files in bedding directorycp $ subjdir / bvecs $ subjdir / bval $ subjdir.bedpostX$ FSLDIR / bin / imcp $ subjdir / nodif_brain_mask $ subjdir.bedpostXif[`$ FSLDIR / bin / imtest $ subjdir / nodif` = 1]: then $ FSLDIR / bin / fslmaths $ subjdir / nodif -mas $ subjdir $ subjdir / nodif_brain_mask.bedpostX / nodif_brainFi# Divide the dataset into several parts againEcho preprocessing stepif [$ gflag -eq 1]; thenpre_command = “$ FSLDIR / bin / split_parts_gpu $ subjdir / data $ subjdir / nodif_brain_mask $ subjdir / grad_dev 1 $ njobs $ subjdir. $ subjdir / data bedpostx”differentpre_command = “$ fsldir / bin / split_parts_gpu $ subjdir / nodif_brain_mask NULL 0 $ njobs $ subjdir.bedpostX”Fiif $ qsys [-eq 0]; then#SGEsplitID = `$ FSLDIR / bin / fsl_sub -T 40 -l $ subjdir.-N bedpostx / logs bedpostx_preproc_gpu $ pre_command`different#PAIRecho $ pre_command> $ subjdir.bedpostX / tempTorque_command = “qsub -V $ queue -k node = 1: ppn = 1: gpus = 1, walltime = 00: 40: 00 -N -o bedpostx_preproc_gpu $ subjdir.bedpostX / logs -for $ subjdir.bedpostX / logs”splitID = `exec $ Torque_command $ subjdir.bedpostX / temp | awk $ 1} ” tail -1 `; professional $ command “$ subjdir> .bedpostX / temptask = “ wc -l $ taskfile ” awk $ 1 ” {print | awk -F. “Print $ 1” Rm $ subjdir.bedpostX / tempDream 10Fiecho $ mergeid> $ subjdir.bedpostX / logs / postproc_IDif [“x $ SGE_ROOT”! = “x”]; then echo replicate $ subjdir type.bedpostX / monitor to see progress. Enter echo $ subjdir.bedpostX / cancel if you want to end all jobs in the queue. Chat $ subjdir.bedpostX / cancel#! / bin / shqdel $ mergeid $ bedpostideoc chmod + x $ subjdir.bedpostX / cancel echo Echo At the end you will try to receive an email related to epost-processing tap. echodifferent Dream 60Fi

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