Re: [Freesurfer] Error with mris_anatomical_stats

Dear Douglas,

The wm.mgz is in the mri folder so it's in:

Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz.

Best Regards, Mahtab.

Sent from myMail for iOS

Thursday, May 19, 2016, 16:19 +0100 from greve@nmr.mgh.harvard.edu greve@nmr.mgh.harvard.edu:

The second one is a valid command (1st is not). What is the full path to the wm.mgz file that is in your anlayzed data?

On 05/19/2016 10:33 AM, Mahtab Farahbakhsh wrote:

...

Dear Bruce,

This is the input command and the output that I get:

bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz

or:

mris_anatomical_stats -l anon/label/lh.BA45.label anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz

This is the SUBJECTS_DIR

export SUBJECTS_DIR=/Applications/freesurfer/experimental_data/TG/anon

cd $SUBJECTS_DIR

Best Regards, Mahtab.

On 19 May 2016 at 13:41, Bruce Fischl < fischl@nmr.mgh.harvard.edu <mailto: fischl@nmr.mgh.harvard.edu >> wrote:

Hi Mahtab

can you please send the screen output of the command you ran and
what it printed, and also what the environment variable
SUBJECTS_DIR is?

cheers
Bruce

On Thu, 19 May 2016, Mahtab Farahbakhsh wrote:

    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?

    Best Regards,
    Mahtab.


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