Try setting the SUBJECTS_DIR to an absolute path, eg, setenv SUBJECTS_DIR `pwd`
On 07/07/2016 05:28 AM, Chatzi, Vasiliki wrote: > > > * > 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 > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
