Hi David - You need to run each of the steps (-prep, -bedp, -path) separately. You can't run them all at the same time. See tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula
Hope this helps, a.y
On Fri, 2 Aug 2013, David Soto wrote:
Hi,
I have successfully run recon-all in my dataset and now am attempting to use trac-all on my diffusion data obtained on a Siemens scanner.
Diffusion dicoms were transformed to .nii using MRIConverter and then to .mnc using
nii2mnc output.nii output_t.mnc.
I am trying to run trac-all on a single subject and for this I have created the configuration file attached (tracula02ST)
As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui and within each subject the T1 serving as input for recon-all are in mri/orig
while the diffusion images are in a folder call diffdata (named output_t.mnc) which also contains the bvecs and bvals files, which were transposed and organised according to the tutorial (named as bvecs_t.txt and bvals_t.txt)
When I run: trac-all -c tracula02ST.txt
I get: ERROR: no analysis step (-{prep,bedp,path}) has been selected
THEN I run: trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so and then gives the long output text below with an error message.
Segmentation fault (core dumped) foreach: No match.
The trac-all.log is attached also.
Could you please help?
Cheers
David