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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