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/
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>>>>>>><bedpost_datacheck.pdf>
>>>>>
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>>
>>----------------------------------------------------------------------
>>-----
>>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
>------------------------------------------------------------------------
>---
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