Hi Marius,
thanks for your help. I just found out why it didn't run successfully. The data files were not in a separate subject subfolder (as I just wanted to analyze one subject), but autoPtx needs a subfolder to work. So "autoPtx_1_preproc data.nii.gz" does not build the correct folder structure for the 2nd step, but "autoPtx_1_preproc example_subject/data.nii.gz" does.
Thanks again,
Kai
On Wed, 27 May 2015 11:11:55 +0000, M. de Groot <[log in to unmask]> wrote:
>Hi Kai,
>
>This file not being there means that the tractography did not run successfully, which seems to agree with the call resulting in a segfault.
>
>Let�s take it from the beginning, there should be a preproc folder, and in that folder, there should be separate folders for each subject in your set, right? Then there should also be a folder for each subject with a .bedpostX suffix, still right? If not, or if in doubt, can you please print (a snippet) of the preproc directory listing (ls -l)?
>
>If this this structure is indeed there, can you list the contents of one of the .bedpostX folders?
>
>Cheers, Marius
>
>On 25 May 2015, at 15:19 , Kai Schlamp <[log in to unmask]> wrote:
>
>> Hello FSL experts,
>>
>> after running successfully autoPtx_1_preproc and autoPtx_2_launchTractography (at least no error messages were presented), the command "autoPtx_prepareForDisplay 0.005" fails with the following error message:
>>
>> Cannot open volume tracts/./ar_l/tracts/tractsNorm for reading!
>> ERROR: Could not open file
>> ==ERROR== Header not recognized. Exiting...
>>
>> And of course that file does not exist. In that directory are only a probtrackx.log and waytotal file. When I run the command in the probtrackx.log file directly I get (after some "sl xx" lines) a segmentation fault.
>>
>> What is wrong here? How can we fix it?
>>
>> We are using AutoPtx 0.1.1 and FSL 5.0.8 under Ubuntu 14.04.
>>
>> Thanks in advance,
>> Kai
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