Dear all,

please find attached the trac-all.log file.

Regards Gerit

On 15 July 2013 18:14, Anastasia Yendiki ayendiki@nmr.mgh.harvard.eduwrote:

Hi Gerit - Can you please send the entire trac-all.log for this subject? There could be some clues in the info that's printed out from the earlier steps, even if there's no outright error in those steps.

Thanks, a.y

On Fri, 5 Jul 2013, Gerit Pfuhl wrote:

...

Dear Freesurfer experts,

for one subject (out of over 80 already processed) I get i nthe last step an error I am unable to locate. The output from the tracula -path command says at the end: option 0 unknown. There are no reported problems in -prep, and -bedp. The script uses default values (I run this subject 3 times, always gets stuck on -path, not before). The subject was processed fine in tracule 5.1.0 with flt. Now in 5.2.0 we use bbr

Excerpt of the output ... /igis/MRI_fs_rec_dti/64-10-**094-1/dlabel/diff/rh.cab_PP_** avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/lh.** ccg_PP_avg33_mni_bbr_cpts_4_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/rh.** ccg_PP_avg33_mni_bbr_cpts_4_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/lh.** slfp_PP_avg33_mni_bbr_cpts_5_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/rh.** slfp_PP_avg33_mni_bbr_cpts_5_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/lh.** slft_PP_avg33_mni_bbr_cpts_5_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/rh.** slft_PP_avg33_mni_bbr_cpts_5_**std.txt ERROR: Option 0 unknown

Thanks for all help to understand this

Gerit

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Hi,

It was set to 7500 in the original dmrirc file. Now I use a file from another subject and changed the dcmlist. Hope that works.

Regards Gerit

On 15 July 2013 20:33, Anastasia Yendiki ayendiki@nmr.mgh.harvard.eduwrote:

Hi Gerit - It seems like the nsample variable is empty. Are you by any chance setting that to something other than the default number in your configuration file?

a.y

On Mon, 15 Jul 2013, Gerit Pfuhl wrote:

Dear all,

...

please find attached the trac-all.log file.

Regards Gerit

On 15 July 2013 18:14, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  Hi Gerit - Can you please send the entire trac-all.log for this

subject? There could be some clues in the info that's printed out from the earlier steps, even if there's no outright error in those steps.

  Thanks,
  a.y

  On Fri, 5 Jul 2013, Gerit Pfuhl wrote:


        Dear Freesurfer experts,

        for one subject (out of over 80 already processed) I get i

nthe last step an error I am unable to locate. The output from the tracula -path command says at the end: option 0 unknown. There are no reported problems in -prep, and -bedp. The script uses default values (I run this subject 3 times, always gets stuck on -path, not before). The subject was processed fine in tracule 5.1.0 with flt. Now in 5.2.0 we use bbr

        Excerpt of the output
        ...
        /igis/MRI_fs_rec_dti/64-10-**094-1/dlabel/diff/rh.cab_PP_**

avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/lh.** ccg_PP_avg33_mni_bbr_cpts_4_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/rh.** ccg_PP_avg33_mni_bbr_cpts_4_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/lh.** slfp_PP_avg33_mni_bbr_cpts_5_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/rh.** slfp_PP_avg33_mni_bbr_cpts_5_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/lh.** slft_PP_avg33_mni_bbr_cpts_5_**std.txt /fastfs/igis/MRI_fs_rec_dti/**64-10-094-1/dlabel/diff/rh.** slft_PP_avg33_mni_bbr_cpts_5_**std.txt ERROR: Option 0 unknown

        Thanks for all help to understand this

        Gerit

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.