Hello Freesurfer Experts, Thanks so much again for all of your help. I am trying to complete the Anatomical ROI Analysis Tutorial because I will need to use segmentation volumes for an experiment we`re running in the lab. In particular, I am trying to complete the group stats files part of the tutorial so that I know how to export this data in the future to excel for statistical analysis. However, I keep getting the following error: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' I have tried to put in my password with sudo, make myself a superuser, and chmod, but nothing seems to work. When I do sudo it will tell me that my SUBJECTS_DIR isn`t defined although it is defined in the first two lines of every terminal window I open (because of my .profile). See here:
IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
[dbm079-066:/Applications/freesurfer/subjects] claire% sudo asegstats2table --subjects 004 008 --meas volume --tablefile aseg_stats.txt
Password:
ERROR: SUBJECTS_DIR environment variable not defined!
Additionally, sometimes I will also see the following error ERROR: output table name should be specified (use --tablefile FILE) after putting in the following: claire% asegstats2table --subjects 004 008 \ --segno 11 17 18 \ --tablefile aseg.vol.txt
ERROR: output table name should be specified (use --tablefile FILE)
Please help! I have tried everything I can think of.
Thank you for everything,
Claire
You are in a folder that you do not have write permission to. Try cding to a different folder, or spec a path to a folder where you have write permissions, eg,
asegstats2table --subjects 004 008 --meas volume --tablefile /tmp/aseg_stats.txt
doug
On 10/30/2014 08:28 AM, Claire Morley wrote:
Hello Freesurfer Experts, Thanks so much again for all of your help. I am trying to complete the Anatomical ROI Analysis Tutorial because I will need to use segmentation volumes for an experiment we`re running in the lab. In particular, I am trying to complete the group stats files part of the tutorial so that I know how to export this data in the future to excel for statistical analysis. However, I keep getting the following error: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' I have tried to put in my password with sudo, make myself a superuser, and chmod, but nothing seems to work. When I do sudo it will tell me that my SUBJECTS_DIR isn`t defined although it is defined in the first two lines of every terminal window I open (because of my .profile). See here:
IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
[dbm079-066:/Applications/freesurfer/subjects] claire% sudo asegstats2table --subjects 004 008 --meas volume --tablefile aseg_stats.txt
Password:
ERROR: SUBJECTS_DIR environment variable not defined!
Additionally, sometimes I will also see the following error ERROR: output table name should be specified (use --tablefile FILE) after putting in the following: claire% asegstats2table --subjects 004 008 \ --segno 11 17 18 \ --tablefile aseg.vol.txt
ERROR: output table name should be specified (use --tablefile FILE)
Please help! I have tried everything I can think of.
Thank you for everything,
Claire
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Claire Morley -
Douglas N Greve