Hi Sandra,
If you call the FDT toolbox from a terminal and then run probtrackx from the GUI, the full script that is called when you press Go appears in the terminal. You can get an idea from this script on how to run probtrackx from the command line.
In the script that you provided, you need to provide the seed mask with -x and the binary mask with -m and also set --opd, so that the path distribution is saved.
Cheers,
Stam
On 20 Oct 2011, at 20:04, Woodman, Sandra wrote:
> Stam/ other FSLers,
>
> I figured out my problem, it is now running. The only thing now that makes me
> weary is that probtrackx in commandline form is taking alot longer to complete
> then when I use the GUI. Do you know if this is normal? Settings that are
> default I didn't include in my command line, because I assumed I did not have
> to. Is this correct? We are using default settings for:
>
> loopcheck. Using curvature threshold of 0.2 (-c), # samples = 5000 (-P), max #
> of steps = 2000 (-S), step lenght= 0.5mm (--steplength).
>
> Thank you!
>
> Sandra
>
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Woodman, Sandra
> Sent: Thu 10/20/2011 2:13 PM
> To: [log in to unmask]
> Subject: Re: [FSL] probtrackx command line help
>
> Stam,
>
> Thank you very much, that was helpful. I believe I now have the command line
> set up properly, but it has failed.
>
> probtrackx --samples=005.bedpostX/merged -m
> ctrl01_sess1_Left-antAL_binarydot5.nii.gz -x nodif_brain_mask.nii.gz
> --dir=Left-antAL --forcedir -o ctrl01_sess1_ptracx_Left-antAL.nii.gz --loopcheck
>
> Log directory is: Left-antAL
> 7
> sl 0
> run
> 58 30 0
> Segmentation fault
>
> Do you know why I would get this fault?
>
> Thanks,
>
> Sandra
>
>
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Stamatios Sotiropoulos
> Sent: Thu 10/20/2011 1:22 PM
> To: [log in to unmask]
> Subject: Re: [FSL] probtrackx command line help
>
> 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
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>>> contains patient information, please contact the Partners Compliance HelpLine
>> at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>>> but does not contain patient information, please contact the sender and
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>>> dispose of the e-mail.
>>>
>>
>> --
>> 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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