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FSL  November 2010

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Subject:

Re: 3 column custom timing file error

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 16 Nov 2010 08:42:54 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (83 lines)

Dear Susan,

OK, so the first thing is that the attached file works fine
for me.  All the events are between 387 and 548 seconds
and are all approximately 5 seconds long.  And there are
19 separate events.  Correct?

Have you been checking whether the files are working
correctly in FEAT, or just looking at them with cat -v ?
I can't see why it wouldn't work unless the numbers
above aren't what you are expecting.

The next point is that there are strange characters in
there.  When I do cat -v I get the following:
387.779	4.347	1^M396.823	5.518	1^M405.866	4.613	1^M414.909	7.078	1^M426.952	3.852	1^M435.994	8.785	1^M448.037	5.678	1^M457.067	4.877	1^M466.099	4.253	1^M475.155	4.853	1^M484.198	5.878	1^M493.322	4.413	1^M502.366	4.253	1^M511.41	3.719	1^M520.453	4.918	1^M529.497	4.052	1^M538.541	6.544	1^M547.586	5.28	1^M

This is indicative of the file being created under Windows
(I assume that is true) as Windows and unix/linux use
different ways of ending the lines.   In Windows it is a
^M character, which you see above, and unix/linux does
not treat this as a proper end of line.  However, FEAT 
reads either format without problems, so that is why it
works for me but I still see strange characters.  If you
do not see these then I guess it is possible that they were
inserted/converted when you attached it to the email
by your email program.  If you do see these characters
and want to get rid of them (as a nicety, because FEAT
will be happy either way) then you can do the following:

cat  PE210E.txt | tr \\r \\n > PE210E_fix.txt

Either way though, it should read this file happily
in FEAT, so please check this and if it does not
then please let us know exactly what is happening
in terms of errors.

All the best,
	Mark



On 16 Nov 2010, at 03:20, Susan Lee wrote:

> Hi Mark,
> 
> Thanks for your prompt reply.  I've already started over and remade this file several times.  I've also renamed a file that does work and fixed the numbers just to see, and that hasn't worked either.  There aren't any strange characters on using your cat command, but the columns aren't appearing as columns, but rather as one continuous row.
> 
> I've attached the file in question here.  Any thoughts?  Thanks so much in advance.<PE210E.txt>
> 
> Susan
> 
> On Nov 13, 2010, at 5:23 AM, Mark Jenkinson wrote:
> 
>> Hi,
>> 
>> Try doing:
>> 
>> cat -v /Users/slee/Kids/PE/TF/PE210E.txt
>> 
>> and looking for unusual characters.  Sometimes
>> they are invisible when viewed in certain ways
>> but can cause problems.
>> 
>> The best chance of fixing it, if you have other
>> files that work OK, is simply to start over and
>> make the file afresh.
>> 
>> All the best,
>> 	Mark
>> 
>> 
>> On 13 Nov 2010, at 06:40, Susan wrote:
>> 
>>> Hi everyone,
>>> 
>>> I've been having a problem with one of my 3-column custom timing files.  I keep getting an error message that reads: "Problem with processing the model: No valid [onset duration strengh] triplets found in /Users/slee/Kids/PE/TF/PE210E.txt child process exited abnormally".
>>> 
>>> I know this happens when you don't follow the right format for the timing files, but I've checked this file several times, and it was created identically to many other files (which had no problems).  I would appreciate any thoughts/advice.
>>> 
>>> Susan Lee.
>>> 
> 

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