Hi - you need to add the --opd flag.
Cheers
Saad
On 25 May 2012, at 18:05, andrew Persichetti wrote:
> Hi all,
>
> I ran probtrackx from the command line. It seems to have ran fine, but I cannot find where it output some of the files.
> there is a 'logdir' directory made in the subjects' directory but it only contains the probtrackx log and the waytotal text file. Where does it put the rest of the stuff (niftiis etc.)?
>
> Below is the command I ran:
>
> # run Probtrackx
> probtrackx --network -s /Volumes/Andrew_HDD/City_fMRI_fsl/${i}/dti/bedpostx.bedpostX/merged -m /Volumes/Andrew_HDD/City_fMRI_fsl/${i}/dti/bedpostx.bedpostX/nodif_brain_mask -x /Volumes/Andrew_HDD/City_fMRI_fsl/fsl_roi_refs/temp_${j}
>
> Thanks!
>
> Best,
> Andrew
>
--
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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