• Hello freesurfer developers,
    I am trying to compute the average_subject template described in the freesurfer wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject).
    I have located all the subjects' directories in one folder named All_data_baseline. Then I set SUBJECTS_DIR to this folder using the command setevn  SUBJECTS_DIR ./ ,and then I defined the subjects using the command setenv SUBJECTS = (subject1 subject2 ...). Finally I run the command make_average_subject --out avgsubject. The directory avgsubject was created but then I received the following error:

    error.log:
    MRISread (.//subject1/surf/lh.sphere.reg): could not open file
    mris_make_template: could not read surface file .//subject1/surf/lh.sphere.reg


    error as it appears on the terminal:
    output subject: avgsubject
    mri_add_xform_to_header -c auto .//avgsubject/mri/mni305.cor.mgz .//avgsubject/mri/mni305.cor.mgz
    INFO: extension is mgz

    tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory
    #@# Making lh registration template ---------
    tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory
    /homedirectory/All_data_baseline/avgsubject
    tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory
    mris_make_template -norot -annot aparc lh sphere.reg subject1

    tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory
    not aligning hemispheres before averaging.
    zeroing medial wall in aparc
    creating new parameterization...

    processing subject subject1 (1 of 313)
    reading spherical surface .//subject1/surf/lh.sphere.reg...
    MRISread(.//subject1/surf/lh.sphere.reg): could not open file
    No such file or directory
    mris_make_template: could not read surface file .//subject1/surf/lh.sphere.reg
    No such file or directory
    ERROR: make_average_surface

    I did search the make_average_subject --help and the mail archive but I have not yet found a solution. Please accept my apologies if there is one but I have not noticed.

    I am using version freesurfer-5.3.0 in a Linux 7.1 with 48 core memory.

    I was wondering if you could possibly provide any advice for troubleshooting this error.

    Best wishes,
    Vasiliki