Re: [Freesurfer] Error with mris_anatomical_stats

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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:

...

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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
  >
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