Hi Cecilia,
you should call the LaunchTractography script from the same folder where you have called the autoPtx_1_preproc script from (that should be the autoPTX folder itself).
Such folder should contain a ‘preproc’ sub-folder, where all the BEDPOSTX results for each subjects are stored.
Check that in the preproc folder the file ‘subjectList’ contains the right paths to your subjects data.
To select the SLF, you need to modify the ‘structureList' file contained in your autoPTX folder.
Cheers,
Matteo
> On 2 Sep 2016, at 12:13, Cecilia Mazzetti <[log in to unmask]> wrote:
>
> Hi all,
> I am using the plugin autoPtx for automated tractography in FSL (using linux) and after the prepocessing steps are done I ran the LaunchTractography script as indicated on the webpage.
> The only problem is that the script doesn't give any output in the terminal (maybe this is not a problem) and only a folder is created in my directory with the first track in the structure List (ar_l) I tried to modify the structure list file (since I only need to extract the superior lingitudinal fasciculi) but again only the first tract of the list is generate d and I can't visualize it either since I get an error saying:
>
> Cannot open volume tracts/bedpostx//tracts/tractsNorm for reading! (infatti TractsNorm non era li')
> ERROR: Could not open file
> ==ERROR== Header not recognized. Exiting..
>
>
> (indeed tractsNorm is not there... I get the feeling that th script doesn't read the all list and consequently is run partially [e.g. Maybe Tracts Norm is generated at the end])
>
> What could be the problem??
> Any suggestions from more expert users??
> Thank you so much in advance for the help
>
>
>
> Best,
> Cecilia
|