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
>
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