Hi Torben - I'm looking at all the invocations of "trac-all -prep" in your log file, and they've both exited with an error (the same bvecs error).

grep prep trac-all.log

-prep -c /Users/torben/Desktop/tracon/tracon New invocation of trac-preproc /Applications/MRSoftware/freesurfer/bin/trac-preproc trac-preproc exited with ERRORS at Do 21 Jun 2012 20:34:41 CEST ... -prep -c /Users/torben/Desktop/tracon/tracon New invocation of trac-preproc /Applications/MRSoftware/freesurfer/bin/trac-preproc trac-preproc exited with ERRORS at So 24 Jun 2012 22:37:30 CEST

After that you've ran "trac-all -bedp" and "trac-all -path", but obviously these are going to fail if "trac-all -prep" has failed. I hope this makes sense.

a.y

On Fri, 29 Jun 2012, Torben Prokscha wrote:

Hi Anastasia!

Yes, we reran trac-all -prep after fixing the bvec issue. I am still surprised how you know that the latest failure was due to a bvecs problem, because the last error message was the one about the missing tract ...?

Thank you for your help!

Best Torben

...

Hi Torben - I just scrolled to the end of your log file. The last invocation of trac-all -prep is the one that failed b/c of the bvecs error. Did you rerun trac-all -prep after you fixed the bvecs?

Thanks, a.y

On Tue, 26 Jun 2012, Torben Prokscha wrote:

...

Hi Priti,

thank you for your reply, but I'm afraid you didn't scroll to the end of the log file: Yes, we had that bvecs/bvals error in the first run, but we corrected it and got the error I reported in my previous mail (it is also printed at the end of the log file):

ERROR: Could not open /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

Could you or anybody else please help with this problem which is obviously related to missing tracts?

Thanks in advance Torben

...

Hi Torben,

Your trac-preproc exited with errors because of the following error.

Error: bvecs and bvals don't have the same number of entries

You should check to see if your bvals and bvecs have the same no.of lines and then rerun trac-all -prep.

Priti

...

Dear all,

while running trac-all, I got the following error:

ERROR: Could not open /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt

Obviously, a similar problem was discussed before (here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.ht...). However, no general solution was publicly mailed. Since it was requested then, I attach the trac-all.log file.

Thanks in advance for any help!

Best Torben Prokscha

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