New subject: sphere.reg file

6 Mar 2020


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Dear freesurfer experts,
I run the following commands to perform analysis with projected
surfaces on my average subject:
make_average_subject --out my_avg_subject --fsgd  fsgd.txt
surfreg --s s_001 --t  my_avg_subject --o my_avg_subject.sphere.reg
mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness
--srcfmt curv --hemi [l/r]h --out  [l/r]h.fsgd.mgh
Theoretically, the mri_preproc function will automatically use the
my_avg_subject.sphere.reg file because I specify my_avg_subject as the
target subject. The problem is that in the output that comes out in
the terminal while this function is running, it is specified that the
file [l/r]h.sphere.reg is selected instead of
[l/r]h.my_avg_subject.sphere.reg.
Additionally, I did a test specifying the flag "--surfreg
my_avg_subject.sphere.reg" in mris_preproc and the values of the
output surface are different from the output that I have when I don't
specify the flag --surfreg in mris_preproc (so, If I don't specify it,
I think that definitely the function doesn't automatically use the
file generated in surfreg, I think the default sphere.reg is used).
What should I do? Is it better to specify the “--surfreg
my_avg_subject.sphere.reg” flag in the mris_preproc function?
Thanks in advance.
Best regards,
Marina.
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what version of freesurfer are you running?
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We are using Freesurfer v6.0
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can you include the previous emails?
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Re: [Freesurfer] sphere.reg file