Hi - we have now released FSL 4.0 and don't use Cygwin any more - we
now use VMPlayer which should improve various things.
Please see www.fmrib.ox.ac.uk/fsl for more details and the FSL 4.0
download.
Cheers.
On 17 Aug 2007, at 11:04, jonathan bosse wrote:
> Hi, I did a full installation of cygwin (there is bc) and
> installed fsl 3.3 and type the lines under cygwin " echo'
> export..." the firstt time I made a mistake so I cleared fslo and I
> tried to do this again and it seem to work but and the cygwin
> terminal it written " bash ./usr/local/fslconf/fsl.sh no such file
> " but it exists in fact I know it is because I probably forgotten a
> spacing the first time but then I reinstalled it carefully (i hope)
> when i type fsl a window is open, but i only can open fslview when
> i clic on FDT or Melodic nothing hapen...
> Someone could please answer me
>
>
>> From: jonathan bosse <[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, 25 Jul 2007 12:12:52 +0200
>>
>> 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-
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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
>>> --------------------------------------------------------------------
>>> ---- ---
>>
>> _________________________________________________________________
>> Personnalisez votre Messenger avec Live.com http://
>> www.windowslive.fr/livecom/
>
> _________________________________________________________________
> Avec Windows Live OneCare éliminez tous les virus de votre PC !
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------------------------------------------------------------------------
---
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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