Hi Anastasia:

You were right. It was the '/' in the file. I did this for the entire list and it worked.

thanks,

Alan

On Thu, Aug 15, 2013 at 3:37 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

Can you please attach the file Forceps_Major_CC.list.txt?

On Thu, 15 Aug 2013, Alan Francis wrote:

Hi Anastasia:

...

Yes the '/' is really there before the autofs. It is puzzling.

thanks,

Alan

On Thu, Aug 15, 2013 at 3:15 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  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/FreeSu rfer_5.3_Data/diffusion_re cons/Forceps_Major_CC.list.txt --overall--tablefileautofs/** space/dali_003/users/BW_**project_DTI/FreeSurfer_5.3_**Data/d iffusion_re cons/Forceps_Major_CC.All.**table

ERROR: thefileautofs/space/dali_003/**users/BW_project_DTI/** FreeSurfer_5.3_Data/diffusio n_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_p roject_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: Thestatsfileautofs/space/dali_**003/users/BW_project_DTI/** FreeSurfer_5.3_Data/dif fusio 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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