Ah, sorry I didn't read that last sentence on backward compatibility :)
You can create the output directory outside probtrackx, the CD into it before calling probtrackx ?
Saad.
On 28 May 2010, at 14:33, Jon Clayden wrote:
> Hi Saad,
>
> Thanks for the quick response.
>
> My problem is that these scripts are run on several systems, not all
> of whose FSL installs I have control over, and some of them are not up
> to date. Doing what you say seems to break on earlier versions, so I
> have a problem with getting the script to run everywhere.
>
> If there's no way around this within probtrackx itself, is there an
> easy way to test what version of FSL is installed?
>
> Thanks,
> Jon
>
> On 28 May 2010 14:15, Saad Jbabdi <[log in to unmask]> wrote:
>> Hi Jon,
>>
>> Yes the -o flag is now the name of the output file for the path distribution, which is now appended to the output directory (--dir).
>> This was a convenient way to allow the user to choose the output file name in both simple and seedmask modes.
>>
>> The way around for you is to get rid of the path and instead just use the baseline file name in the -o flag.
>>
>> Saad.
>>
>>
>> On 28 May 2010, at 13:53, Jon Clayden wrote:
>>
>>> Dear all,
>>>
>>> I've (belatedly) updated FSL from version 4.1.4 to 4.1.5 (on Mac OS
>>> X.5.8), and some of my scripts are now running into problems which
>>> seem to be related to the naming of output files by probtrackx. Did
>>> these change in this patch?
>>>
>>> The command I use is below [1]. As far as I remember this form has
>>> worked fine since v4.0.0, with the effect that visitation maps were
>>> created as ".../fdt.track/IMAGE_x_y_z.nii.gz". But now I get the error
>>> shown underneath [2]. It seems that probtrackx now puts the value of
>>> the -o flag after that of the --dir flag to establish its output file,
>>> but if both are given as full paths, as here, then this clearly
>>> doesn't work.
>>>
>>> My question is, assuming something did change in FSL 4.1.5, is there a
>>> way around this problem *which is backwards compatible with earlier
>>> versions of FSL*?
>>>
>>> Thanks in advance.
>>>
>>> All the best,
>>> Jon
>>>
>>> --
>>>
>>> [1]
>>> /usr/local/fsl/bin/probtrackx --opd
>>> --dir=/Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE
>>> --mode=simple -x
>>> /var/folders/i4/i4QIhI5kER4SK2fLTGygV++++TM/-Tmp-/RtmpBSKMVk/file10d63af1
>>> --forcedir -s /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.bedpostX/merged
>>> -m /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.bedpostX/nodif_brain_mask
>>> -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 -o
>>> /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE
>>>
>>>
>>> [2]
>>> Log directory is:
>>> /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE
>>> 1_1
>>> 1_2
>>> 1_3
>>> 7
>>> 48 57 13
>>> Error: failed to open file
>>> /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE//Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE_48_57_13.nii.gz
>>> ERROR: Could not open image
>>> /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE//Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE_48_57_13
>>> Image Exception : #23 :: Failed to open volume
>>> /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE//Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE_48_57_13
>>> for writing
>>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>>>
>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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