[Freesurfer] add subject to group but cannot find brain for 049

2011-03-31 Thread Knut J Bjuland
I have added a subject to the to the groups of subject that was available for the qdec tutorials. with this in mind I have used make_average_subject and I have now 41 subject. But when I run this command there is always a subject for which it can not find brain. I am positive that the necessary

Re: [Freesurfer] add subject to group but cannot find brain for 049

2011-03-31 Thread Bruce Fischl
can you run ls -l to check that that file exists and you have permission to it? Also, we need the command line you ran and the error you got in order to help you. cheers Bruce On Thu, 31 Mar 2011, Knut J Bjuland wrote: > I have added a subject to the to the groups of subject that was > availabl

Re: [Freesurfer] add subject to group but cannot find brain for 049

2011-03-31 Thread Knut J Bjuland
Hi I used the followinf commando line optin for make_average_subjects --fsgd gender_age.fsgd --out fsaverage. I have now used chmod -R +w * to add write permission to the dir below. As a matter of fate I ran make_average_subject --subjects 004 --out test and got the same error as before. Kn

Re: [Freesurfer] add subject to group but cannot find brain for 049

2011-03-31 Thread Bruce Fischl
and what is the error? On Thu, 31 Mar 2011, Knut J Bjuland wrote: > Hi > > I used the followinf commando line optin for make_average_subjects --fsgd > gender_age.fsgd --out fsaverage. I have now used chmod -R +w * to add write > permission to the dir below. As a matter of fate I ran make_average

Re: [Freesurfer] add subject to group but cannot find brain for 049

2011-03-31 Thread Knut J Bjuland
i used the following command to repeat a failure output. i used just one subject to get a fast output since my pc is just a core i5 box. make_average_subject --subjects 004 --out test INFO: extension is mgz ERROR: cannot find brain for 004 ERROR: make_average_volume It appears that the tutorials

Re: [Freesurfer] add subject to group but cannot find brain for 049

2011-03-31 Thread Douglas N Greve
That is probably the case that 004 does not have all its files. Some of the files have been removed to make the distribution smaller. There may only be enough data to run the tutorial. doug Knut J Bjuland wrote: > i used the following command to repeat a failure output. i used just one > subjec

Re: [Freesurfer] add subject to group but cannot find brain for 049

2011-04-01 Thread Bruce Fischl
Hi Knut does the file brain.mgz exist in $SUBJECTS_DIR/004/mri? If so, can you run ls -l $SUBJECTS_DIR/004/mri/brain.mgz Bruce On Thu, 31 Mar 2011, Knut J Bjuland wrote: > i used the following command to repeat a failure output. i used just one > subject to get a fast output since my pc is