Re: [Freesurfer] Error with mris_anatomical_stats

can you run mri_info on it? And please include the full screen output including the command line that you run as well as what it produces.

thanks Bruce On Fri, 24 Aug 2018, Davide Momi wrote:

External Email - Use Caution

Yes, I meant the second one and rh.aparc.annot (not lh) given that as you said I specified rh.

As for the ls -l on wm.mgz this is the output:

-rw-------@ 1 davidemomi  staff  432151 Jun 13  2017 wm.mgz

Thanks

Il giorno ven 24 ago 2018 alle ore 17:35 Bruce Fischl fischl@nmr.mgh.harvard.edu ha scritto: Hi Davide

  do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It should be the
  latter, not the former. Also, can you send us the output of ls -l on the
  wm.mgz? And finally, you probably want to use rh.aparc.annot not
  lh.aparc.annot since you specified rh on the command line

  cheers
  Bruce


    On Fri, 24 Aug 2018, Davide Momi wrote:

  >
  >         External Email - Use Caution        
  >
  > Dear Bruce, 
  >
  > thanks for your response. 
  >
  > my SUBJECTS_DIR is set to:  /Users/davidemomi/Downloads/Broad_60_AV, which is actually
  where the
  > output of recon-all is located. 
  >
  > the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory
  >
  > Thanks again 
  >
  >
  >
  >
  > Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl <fischl@nmr.mgh.harvard.edu> ha
  scritto:
  >       Hi Davide
  >
  >       does that file exist? What is your SUBJECTS_DIR set to?
  >
  >       cheers
  >       Bruce
  >       On Fri, 24 Aug 2018,
  >       Davide Momi wrote:
  >
  >       >
  >       >         External Email - Use Caution        
  >       >
  >       > Dear FreeSurfer,
  >       >
  >       > I have a problem when I use mris_anatomical_stats. It gives me an error saying
  that it
  >       couldn't read
  >       >  the input volume which is the wm.mgz file.
  >       > would you please help me how I should fix this problem?
  >       > this is the command which I used: 
  >       >
  >       > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh
  >       >
  >       > computing statistics for each annotation in label/lh.aparc.annot.
  >       >
  >       > reading volume /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...
  >       >
  >       > mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1): could
  not open
  >       file
  >       >
  >       > mris_anatomical_stats: could not read input volume
  >       > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz
  >       >
  >       >
  >       > Thanks in advance
  >       >
  >       >
  >       > Davide 
  >       >
  >       >_______________________________________________
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >       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/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.
  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


  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/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.