Hi,
Yes, I think removing -u from the sort should be safe for
this usage in eddy_correct. If it does go wrong then the
problem will be that it creates an output that includes
duplicate images, and hence looking at the number of
timepoints in the eddy_correct output will show whether
this has gone wrong or not.
So do try and edit the file $FSLDIR/bin/imglob for now.
However, I agree that as this problem hasn't come up
before then there is probably something strange with
your cygwin installation and you should check that.
All the best,
Mark
On 5 Feb 2007, at 19:33, Tim Behrens wrote:
> OK - I know what is happening here.
> Unfortunately, your cygwin has a strange version of a program
> called sort, which is used by a program called imglob, which is
> used in eddy_correct.
>
> It is quite common in cygwin for programs to have non-standard
> usages, but I have not seen this one before, and I am pretty sure
> other people use eddy_correct on cygwin, so you might want to check
> your cygwin installation.
>
> The problem is that your "sort" program does not recognise the "-u"
> command. It should!
>
> Anyway, I am pretty sure you can fix this by going into the
> following file (with a text editor inside cygwin, like emacs):
>
> $FSLDIR/bin/imglob
>
> and removing the -u on the penultimate line.
>
> MJ - will this work? I've done a few tests, and it looks like it
> will.
>
> Anyway, if you save that changed file, eddy_correct should work.
>
> If you are having trouble, we can send you a changed version of the
> file.
>
> Cheers
>
> T
>
>
>
> On 5 Feb 2007, at 17:49, Tim Behrens wrote:
>
>> Strange -
>> can you run the following:
>> avwinfo Image4d
>>
>> and
>>
>> avwmaths Image4d -r -R
>>
>> Thanks
>>
>> Tim
>>
>> On 5 Feb 2007, at 17:04, Dianne Patterson wrote:
>>
>>> Dear Group,
>>>
>>> I am just starting to experiment with fsl for dti.
>>> I tried eddy-correct, which seems to work but generates a
>>> complaint that it cannot find the file...
>>> Should I be concerned? What is it talking about?
>>> (WinXP_Pro, cygwin -from the fsl site, fsl test data runs
>>> alright, fsl 3.3)
>>> The img hdr pair was generated by DTIstudio and includes the B0
>>> values-volumes 0 and 1 and the diffusion volumes 2-26.
>>>
>>> [dpat@abel ~/EddyTest]$ ls
>>> Image4d.hdr Image4d.img
>>> [dpat@abel ~/EddyTest]$ eddy_correct Image4d.img test1 0
>>> -uThe system cannot find the file specified.
>>>
>>> Usage: avwmerge <-x/y/z/t> <output> <file1 file2 .......>
>>>
>>> -t : concatenate images in time
>>> -x : concatenate images in the x direction
>>> -y : concatenate images in the y direction
>>> -z : concatenate images in the z direction
>>>
>>> -a : auto-choose: single slices -> volume, volumes -> 4D (time
>>> series)
>>>
>>> [dpat@abel ~/EddyTest]$ ls
>>> Image4d.hdr Image4d.img test1.nii.gz
>>>
>>> Thankyou for your time,
>>>
>>> Dianne
>>>
>>>
>>> --
>>> Dianne Patterson, Ph.D.
>>> [log in to unmask]
>>> ERP Lab
>>> University of Arizona
>>> 621-3256 (Office)
>>
>
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