* 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