Can you send the log file (should be in the scripts dir).

doug

nitenson@nmr.mgh.harvard.edu wrote:

Hi,

I'm a newcomer to Freesurfer and I'm having problems trying to create

an average subject from a subset of our patients. I used the command "make_average_surface --fsgd y.fsgd" with y.fsgd basically being a copy of an old fsgd file with a few subjects deleted. The process ran for several hours (I had to let it run over the weekend) and seemed to be processing the 12 subjects that I wanted. However when I tried to open it today with "tksurfer 12AboveChanceAvg lh inflated", I get the following message:

surfer: current subjects dir: /space/sake/3/users/inverse/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/homes/006/nitenson ERROR: could not read header info from T1 or orig in /space/sake/3/users/inverse/subjects/12AboveChanceAvg/mri

I noticed that the mri folder in the new average I created only has one mgz file (mni305.cor.mgz) while the mri folder in fsaverage has many more.

I am currently running make_average_subject --fsgd y.fsgd, but it seems that it's starting to produce the same results.

What is the best way to create an average subject on which to study functional overlays?

Thanks,

Adam Nitenson Brain Genomic Lab

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