External Email - Use Caution
Assuming that you have set SUBJECTS_DIR to a path where you have read/write permission, then I wonder if you have an alias defined in your shell such that the rm command contains “-I” (the interactive switch) which would force rm to ask you for permission every time it wants to remove something. Type “alias” into your shell prompt and see if something shows up for the remove command. If so then I would remove that alias from your environment with unalias.
$ alias... look for output containing rm -i ...
$ unalias rm
-R
On Mar 31, 2025, at 20:48, Bedard, Patrick (NIH/NINDS) [C] <patrick.bedard(a)nih.gov> wrote: External Email - Use Caution Hello all I’m running the recon-all tool : recon-all -all -sd . -subjid FS -i ${subj}_T1_al.niiIt works fine, but at some point, the program stops and asks at the terminal: writing to orig_nu.mgz...rm: descend into write-protected directory './tmp.mri_nu_correct.mni.41843'? yrm: remove write-protected directory './tmp.mri_nu_correct.mni.41843'? y and I have to answer “y”,but if I’m not checking it just sits and waits and take so much time… do you have any idea what might case that?I have all the permissions on the directories. BestPatrick ===================Patrick Bédard, PhD, [C]ScientistNational Institutes of HealthNational Institute of Neurological Disorders and Stroke _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
