Are you in the C001 directory when you run the command? Can you send the terminal output?

Ed Gronenschild wrote:

Hi,

I'm trying to use mri_segstats and get the following error:

ERROR: could not open stats/aseg1.stats for writing

The full command I gave was:

mri_segstats --seg mri/aseg.mgz --sum stats/aseg1.stats --pv mri/ norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity- units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab / Applications/freesurfer/ASegStatsLUT.txt --subject C001

The SUBJECTS_DIR was set to the directory containing the subject C001. I have full privileges to read/write to all folders.

If I try to write to just aseg1.stats (so using option --sum aseg1.stats) I get the error message that aseg.mgz could not be opened.

I'm on a Mac using FreeSurfer v5.0.0.

Ed

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