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Hi, I ran into trouble with an infinite loop as well, but for me, it was always the last slice to be processed. This happened because there was no output stored for one slice (slice 0 for me, because I had aborted processing at that point), and so the ouputs couldn't be merged. When I started bedpost again, the software seems to have looked up the slices that already had log-files, and didn't process these. And of course it couldn't merge afterwards because the slice still had no output! Solution was easy for me: delete (or rename) the bedpost directory (maybe deleting the log-file would help as well, but this came to my mind too late...) Hope this helps you. Kerstin ----- Original Message ----- From: jonathan bosse <[log in to unmask]> Date: Wednesday, July 25, 2007 8:12 pm Subject: Re: [FSL] Bedpost trouble > Hi, > I tried to change bedpost_proc but it doesn't seem to work ( in > fact Iwit > 10-12 hours and I stoped it because it has only processsed the > first slice > (Windows xp 3.20GHz (2processors), 1 Go ram) I don't know if it's > normal > that it took so much time, I intend to deal with 40 slices data so > I don't > to wait 400 h). > I tried it on linux and it seemed to work since it was written " 0 > slices > processed ... DONE" but on the desktop there was a window with > Bedpost and > a clock showing that it was still processing Icouldn't close it , I > close > linux (doublr ot window/linux) and reboot the computer but i can't > open > linux now. > So, I don't if it's because I didn't wait enough or because It > simply > doesn't work. > > >From: Steve Smith <[log in to unmask]> > >Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > >To: [log in to unmask] > >Subject: Re: [FSL] Bedpost trouble > >Date: Wed, 18 Jul 2007 18:42:47 +0100 > > > >Some linux flavours don't have bc; with "our" distribution of > Cygwin, you > >definitely get bc if you do a FULL install (i.e. follow the > instructions > >and install all packages). > >Steve. > > > > > > > >On 18 Jul 2007, at 18:40, Saad Jbabdi wrote: > > > >>Hi, > >>Your data seem fine, although you need to flip your bvecs in the > x- > >>directions (see dti_V1 using line mode). > >> > >>bedpost won't work for you if you don't have bc, as it has a loop > inside > >>that increments slice numbers. > >>I don't know why you don't have bc (especially when you use linux). > >>I quick and dirty fix for you would be to change the file > $FSLDIR/ > >>bin/bedpost_proc > >> > >>replace the line: > >> >> slice=`echo "$slice +1" | bc` > >>with the line: > >> >> let "slice+=1" > >>or with > >> >> slice=`expr $slice + 1 ` > >> > >>This should do the trick. Let us know how it goes? > >> > >>Saad. > >> > >> > >>On 18 Jul 2007, at 14:25, jonathan bosse wrote: > >> > >>>Hi > >>>I send the data on the website (555 433) . > >>>But I don't understand what should I do with the version of > Cygwin (this > >>>one on the site isn't good ? we have installed it on diffrents > machines > >>>(1 or 2 processors and it doesn't seemed to work) > >>>) . In cas I found the bc program what should I do with it ? > >>>I'll be very happy if someone could answer me precisely > >>>thanks. > >>> > >>> > >>>>From: Tim Behrens <[log in to unmask]> > >>>>Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > >>>>To: [log in to unmask] > >>>>Subject: Re: [FSL] Bedpost trouble > >>>>Date: Tue, 17 Jul 2007 16:06:12 +0100 > >>>> > >>>>Hi - > >>>>Is it the case that the problem is the same on the linux and > cygwin > >>>>machines. > >>>>If so, could you upload the input data directory and the > bedpost > >>>>directory onto our system > >>>>www.fmrib.ox.ac.uk/cgi-bin/upload.cgi > >>>> > >>>>and send us the relevant number > >>>> > >>>> > >>>>Thanks > >>>> > >>>>Tim > >>>> > >>>>On 17 Jul 2007, at 14:04, jonathan bosse wrote: > >>>> > >>>>>Hi, > >>>>>the version of cygwin that we have is the one with a link on > 'your' > >>>>>web site (http://fsl.fmrib.ox.ac.uk/fsl/) but the problem is > that it > >>>>>doesn't work with Linux too, I 've got the same problem (i > think it > >>>>>is but i'm not sure : it seeems like fsl could not process > any second > >>>>>slice) (it is always written " 0 slices processed .... 1 > slices > >>>>>processed....1silces processed...1slices processed.... > 1slices.....).>>>>>I found a bc-1.06 progam for cygwin. > >>>>>sorry, I don't understand what do you mean with 'put it in > your path' > >>>>>thanks. > >>>>> > >>>>> > >>>>>>From: Tim Behrens <[log in to unmask]> > >>>>>>Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > >>>>>>To: [log in to unmask] > >>>>>>Subject: Re: [FSL] Bedpost trouble > >>>>>>Date: Tue, 17 Jul 2007 12:28:21 +0100 > >>>>>> > >>>>>>Hi - the problem is that your cygwin OS cannot see a program > called > >>>>>>bc. This is a standard program in UNIX distributions. > >>>>>> > >>>>>>This either means that you installed a lightweight version of > cygwin > >>>>>> that does not contain bc, or that your version of bc is > not in > >>>>>>your path. > >>>>>> > >>>>>>If it is the former, you either need to completely reinstall > cygwin, > >>>>>> and choose the_complete_ installation, i.e. "select all", > or find > >>>>>>a version of bc for cygwin, and put it in your path. > >>>>>> > >>>>>>Cheers > >>>>>> > >>>>>>T > >>>>>> > >>>>>>On 17 Jul 2007, at 11:04, jonathan bosse wrote: > >>>>>> > >>>>>>>thanks for the reply > >>>>>>>DTIFIT works on my data. > >>>>>>>I send bedpost_datacheck > >>>>>>>thanks. > >>>>>>> > >>>>>>> > >>>>>>>>From: Tim Behrens <[log in to unmask]> > >>>>>>>>Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > >>>>>>>>To: [log in to unmask] > >>>>>>>>Subject: Re: [FSL] Bedpost trouble > >>>>>>>>Date: Tue, 17 Jul 2007 10:33:20 +0100 > >>>>>>>> > >>>>>>>>Hi - does dtifit work ok on your data? > >>>>>>>>And can you send the output of bedpost_datacheck > >>>>>>>> > >>>>>>>>Thanks > >>>>>>>>T > >>>>>>>> > >>>>>>>>On 17 Jul 2007, at 09:43, Jonathan Bosse wrote: > >>>>>>>> > >>>>>>>>>Hi, > >>>>>>>>>I'm trying to do a bedpost ( 18 directions, 3 and 40 > (target) > >>>>>>>>>slices) band > >>>>>>>>>I wait more than 3 days (for 3 slices) even with cygwin or > with > >>>>>>>>>Linux, > >>>>>>>>>when I'm looking to the *.bedpost directory, I can see > only the > >>>>>>>>>first > >>>>>>>>>slice (with linux it's written "0 slices processed... 1 > slices>>>>>>>>>processed... 1 slices processed... 1 slices > processed (again and > >>>>>>>>> again)". > >>>>>>>>>I've run the feeds and it seems to work (there's an error > message > >>>>>>>>> but > >>>>>>>>>there's a result) (the feeds data has only 1 slice) (but > > >>>>>>>>>tractography in > >>>>>>>>>only one slice isn't very significant). > >>>>>>>>>But all the other functions of fsl seemed to work (fdt, > melodic..)>>>>>>>>>So I join the fslerrorreport of my data (18 > directions, 3 slices). > >>>>>>>>>Thank you for the help. > >>>>>>>>><fsl_nab4aS.gz> > >>>>>>> > >>>>>>>_________________________________________________________________ > >>>>>>>Windows Live Messenger sur i-mode? : dialoguez avec vos amis > depuis > >>>>>>> votre mobile comme sur PC ! http://mobile.live.fr/ > >>>>>>>messenger/bouygues/ > >>>>>>><bedpost_datacheck.pdf> > >>>>> > >>>>>_________________________________________________________________ > >>>>>Gagnez des écrans plats avec Live.com http://www.image-addict.fr/ > >>> > >>>_________________________________________________________________ > >>>Découvrez le Blog heroic Fantaisy d'Eragon! http://eragon-heroic- > > >>>fantasy.spaces.live.com/ > >> > >>------------------------------------------------------------------ > ---- > >>----- > >>Saad Jbabdi, > >>Postdoctoral Research Assistant, > >>Oxford University FMRIB Centre > >> > >>FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > >>+44 (0) 1865 222545 (fax 222717) > >>[log in to unmask] http://www.fmrib.ox.ac.uk/~saad > >>------------------------------------------------------------------ > ---- > >>----- > >> > >> > >> > >> > > > > > >------------------------------------------------------------------- > ----- > >--- > >Stephen M. Smith, Professor of Biomedical Engineering > >Associate Director, Oxford University FMRIB Centre > > > >FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > >+44 (0) 1865 222726 (fax 222717) > >[log in to unmask] http://www.fmrib.ox.ac.uk/~steve > >------------------------------------------------------------------- > ----- > >--- > > _________________________________________________________________ > Personnalisez votre Messenger avec Live.com > http://www.windowslive.fr/livecom/ >