that's weird. I'm not sure what to do. The log says that it is creating T1.mgz and not t1.mgz. Can you try this:

cd $SUBJECTS_DIR/subject/mri mri_normalize -g 1 nu.mgz T1.mgz

this should create T1.mgz and not t1.mgz

doug

tulu wrote:

Dear FS experts and Prof. Douglas N Greve, Here is log file. I work on other machine under CentOS 5 and FS 4.5 version but I copy the result from this machine to other machine and find it only have t1.mgz rather than T1.mgz. I guess is the language system problem ? Finally I use a short matlab script to change t1.mgz name as T1.mgz.

Thanks in advance Best JLH

-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, June 13, 2011 11:01 PM To: tulu@ms36.hinet.net Cc: freesurfer Subject: Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

Do you mean your individual subject after running through FS has a file called t1.mgz and not T1.mgz? Something is definitely wrong there. Can you send the log file? doug

tulu@ms36.hinet.net wrote:

...

Dear FS experts, I use FS5.1 and previous data run on other machine. When I try to make_average_subjects program, I get error message that it can not get T1.mgz data from subject folder. When I check my dataset, actually it has t1.mgz rather than T1.mgz. how could I change the setting from T1.mgz to t1.mgz thanks help JLH

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