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
properly
> 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
|