Yes, that might be a good bet. Cheers.
Jon
On 28 May 2010 14:36, Saad Jbabdi <[log in to unmask]> wrote:
> 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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