I didn't suggest taking it off, I meant make sure that the '/' is there, because the error message suggested to me that a '/' was missing from a filename listed IN that text file. Check your original error message.

On Thu, 15 Aug 2013, Alan Francis wrote:

Hi Anastasia:

I took off the '/' before the autofs, but then it gave me a different
problem.

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : tractstats2table --load-pathstats-from-fileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re
cons/Forceps_Major_CC.list.txt --overall --tablefileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re

cons/Forceps_Major_CC.All.table

ERROR: the fileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re
cons/Forceps_Major_CC.list.txt doesnt exist

Actually it does exist.

thanks,

Alan


On Thu, Aug 15, 2013 at 2:40 PM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:

      Is it really autofs without the '/' in front?

      On Thu, 15 Aug 2013, Alan Francis wrote:

      Hi Anastasia:

      Sorry to bother you again. I am trying to extract trac
      stats from the FS
      data. When I run the following script, it gives me an
      error message:

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5
      .3_Data/diffusion_
      recons] : tractstats2table--load-pathstats-from-file/autofs/space/dali_003/users/BW_project_DTI/FreeS
      urfer_5.3_Data/diffusion_r
      econs/Forceps_Major_CC.list.txt --overall--tablefile/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/

      diffusion_r
econs/Forceps_Major_CC.All.table

Parsing the .stats files

ERROR: The statsfileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusio
n_re
cons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
is not found
or is too small to be a valid statsfile

However, when I manually checked the pathstats.overall.txt, the
data is
physically there. Am I doing something wrong?

thanks so much,

Alan




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