Hi Sandra,
Yes, you need to provide both. The mask is the binary brain mask you get from BET, after skull stripping. The --samples should point to the bedpostX output files, normally named as "merged_*". So if you are running tractography from the bedpostx directory you need to set --samples=merged or --samples=bpx_dir/merged in general, where bpx_dir is the bedpostx directory.
Cheers,
Stam
On 20 Oct 2011, at 17:41, Woodman, Sandra wrote:
> Hello,
>
> Thanks for the response. So I need to use a seed volume and a mask? Also for
> the --samples argument, what is the "basename of sample files" refering to?
> What are the sample files?
>
> I appreciate your help,
>
> Sandra
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Saad Jbabdi
> Sent: Thu 10/20/2011 4:29 AM
> To: [log in to unmask]
> Subject: Re: [FSL] probtrackx command line help
>
> Hi Sandra
> You are missing two out of the three compulsory arguments.
> Please type probtrackx then press [enter] in a terminal for a list of command
> line arguments.
>
> Saad
>
> On 19 Oct 2011, at 17:51, Woodman, Sandra wrote:
>
>> Hello!
>>
>> We run probtrackx using the Fdt GUI, and now want to try running the same
> thing
>> with the command line. I am currently having some problems with the setup.
>>
>> Specifications:
>> We are using a binary mask of a seedregion (when we use the GUI, under 'seed
>> space' we select 'single mask'). We use loopcheck. Using curvature threshold
>> of 0.2, # samples = 5000, max # of steps = 2000, step lenght= 0.5mm...I
> believe
>> those are all default so do not need to be in command line?
>>
>> Being run in a subjects individual bedpostX directiory: Here is my latest
>> attempt:
>>
>>
>> [purkinje:005.bedpostX] (nmr-stable5.1-env) probtrackx -m
>> ctrl01_sess1_Left-antAL_binarydot5.nii.gz --dir=Left-antAL --forcedir -o
>> ctrl01_sess1_ptracx_Left-antAL.nii.gz --loopcheck
>>
>>
>> When I enter this into a terminal I get no error reports, it just shows me the
>> text from probtrackx --help.
>>
>>
>> Am I doing something wrong? Is there something I am not specifying?
>>
>>
>> Any help/suggestions are much appreciated,
>>
>> Sandra
>>
>>
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>
> --
> 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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