Hi Bernd, which version of FS are you using? make_average_subject did not always produce a tif file, but the FS 5.1 version should have. If not, you can use mris_make_template (this is what is called inside of make_average_subject). doug

On 10/29/12 2:14 AM, Bernd Merkel wrote:

Dear all,

just having started using Freesurfer, I have the following question which has also been touched by other people but I couldn't find a solution for my problem.

I have about 100 subjects from which I want to create my own template to be used by Freesurfer. These have been my steps:

1. recon-all (on all my subjects)

2. make_average_subject --subjects (list of all subjects)

3. I wanted to use the code provided on the Wiki:

for subject in 'subjectList.txt'; do cd $SUBJECTS_DIR/subject mris_register -curv surf/lh.sphere $SUBJECTS_DIR/newtemplate/lh. reg.template.tif surf/lh.sphere.reg.newtemplate end

The first two steps went fine. But I do not know how to handle that template.tif-File, because that hasn't been created as a result during my second step. Have I missed something ? Furthermore there is this other command

mris_make_template

but I do not know whether (and where in my processing) I should use that (perhaps instead of make_average_subject) ? Thanks for any help, Bernd

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