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>
>>>>>>
>>>>>> _________________________________________________________________
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>>>>>> depuis votre mobile comme sur PC ! http://mobile.live.fr/
>>>>>> messenger/bouygues/
>>>>>> <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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