Hi Mahtab
the mris_anatomical_stats help says:
mris_anatomical_stats [options] <subjectname> <hemi> [<surfacename>] . . . -f <tablefile> table output to tablefile (different format than -b). Must use-a or -l options to spec input. . . .
so you are specifycing the name of the table as "anon", the name of the subject as "lh", the name of the hemi as "anon" and the surface name as "lh".
On Thu, 19 May 2016, 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 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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