External Email - Use Caution Dear all
I solved this. In case it is useful for someone else: the load_mgh needs a temp dir in case the input is a mgz, to store the unzipped file. To set the tmp dir, set the TMPDIR or TEMPDIR evnironment variable, otherwise /scratch is used if present. But in my case is not writable, so the command fails. Bests, Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1ItIv-jpXPnKALveycIN_yCP1Wp9_oFtdN4jy1RIHA83-o31Cy2mSJcT8M2S_q4dp_Z8oRNm-hENpAVwD_qRb5u6GkiytWak4YPXaHwUqtDPZ61l0RBBGgb9E066DMid2u6Ev2-6blo1DUf0OEXna4dhXN-z1IQrs4UzpHPckiAldJJSBBqCkAEuJmto2MIm3ktiJIZoyeiu7FZt0STZftOf_SpbB-nL_ZP1ojAwMVyJh7wPF55f1VnNZaBJJwXgi/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1YdALusv0t23JR3fYBLLwG3oCI0mqdrqdgc2lSNI9nb8_fmAMEBd78xbijVAGXDBUdUd6NXr-dyxmcTtLcql_WoOGpajUNtthF5wQ5iIoaBAOlWgAuJLZ85_S3AWiLuzAqNlIOuh9OJHq3JEpvz5BP-0aFnTy2_Nmx5o-F65qpT50CJofnAcl2acjX7LJpG2IdQo_0PON-rlnrFH7CJXD45cVseetAT4dHZMbUdNPnTSvCNjgsgBf9UdKBOsH86kB1L-bKqZc2Upyyxb-NoVm7A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1PrHoaa5WUgaOOBPnzVAQS0WI8U9TsSL1jud9E_uaAs-u_NwNRGdyunfE9oIRiWgCmOdSkmWmcOBElEuHoI1D4c-_JiK33GiJYlD3OWX8vgJdWm7nZqtCl2_9NGF_KCMygtLvcOVZHI4x6sEOPSijrIULIcKGegp00B11iXSVYUl6zI-D0y8rOzZYJmsm26NYHh8bI9zP55ZQnqPDt7DDeJNH8Qus4d8piYdjxp3fma7TEVF1KyjdhYaPlNoXBX9I87xb2XeEx4iRZu8TyrdemQ/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1PrHoaa5WUgaOOBPnzVAQS0WI8U9TsSL1jud9E_uaAs-u_NwNRGdyunfE9oIRiWgCmOdSkmWmcOBElEuHoI1D4c-_JiK33GiJYlD3OWX8vgJdWm7nZqtCl2_9NGF_KCMygtLvcOVZHI4x6sEOPSijrIULIcKGegp00B11iXSVYUl6zI-D0y8rOzZYJmsm26NYHh8bI9zP55ZQnqPDt7DDeJNH8Qus4d8piYdjxp3fma7TEVF1KyjdhYaPlNoXBX9I87xb2XeEx4iRZu8TyrdemQ/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 ________________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Bernardoni, Fabio <fabio.bernard...@uniklinikum-dresden.de> Gesendet: Mittwoch, 30. Juni 2021 14:07:34 An: freesurfer mailing list Betreff: [Freesurfer] problem with mris_compute_lgi External Email - Use Caution Dear FS experts, when running mris_compute_lgi, the make_outer_surface step produces an error: >> reading filled volume... /bin/bash: /scratch/tp81860215899812157.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp81860215899812157.load_mgh.m.mgh for reading Looking more closer at what produces the error, it is the MRIread function: vol=MRIread('..../surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz') /bin/bash: /scratch/tp81861321896965219.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp81861321896965219.load_mgh.m.mgh for reading ERROR: loading ..../surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz as MGH vol = [] I do not understand where the /scratch/tp81861321896965219.load_mgh.m.mgh is created/located. Is it within the rh.pial.filled.mgz? Even going through the MRIread function I couldn't figure out. Maybe the error is actually in the mri_fill step (that however exits with no error) Thanks in advance for any hint Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1j3t_3Y4iFjkXouNEHQLd1euJWlTzdWEoUG3WoZLDjonBHv-KC04b7EqMEFAWM6bEAmyZN0IafZm8SgPcMYm43qeyeXA4CYElHMpK89qLgXTNS-MQpG4H1WfpBcdxiNKqBr49CFP89JJi4Gtf5uHkwMLMEpKN_3k3vvn6uOxKqxhZJX9fzQNqyogMHYRz-PMiNwBiiVG_fUJL1Ul0nXv7o8Sr4vcojTAOci8RL3rCR_w_8iCgkX3bXB0gb-oP3QhF/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1uAkOO7CtOzygpinM5tt9ZZHkhl_HV3HHZnI2wodEWKz8oNE1Y8bMnmCGBXt6F84SHWDhazmLk1mUGMAJABTUzGRAikxjiRElPVtx7QgBCQZi7_QAQpjILl3qi7rTZXwMLCY1PUT6XgKVGtIu7rxtTB0oGeaPes-lP5exBt8u8vNagtSKDKsd13NfA7nkwes1NiGb3G3CgF8gUZB9x7uXox-xI0OfScQpicSCmeMBV4O_Y0Dpecahs3iPsS0gPokazpqM2kxOd93GP6gFRjDSuA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1GIWqSkZNuXf_zg2CrESTkx8X0PW_gl1iao4QNgyhxPTCr3ZL5J71TSbomlWf7Vy722LMZLcaKu37Y6DpAJj59r-v1fJwe86US5FvwPWVjizzB87BvqB0O6BixNXiqYBZmb8f6rAlj-3FeyYr8KFHgvNlFnwZz8t9WQ_sh0NLiBTM8o8Mr580kDzMeDrjbfRqNcSxVZytpDkyQPMOvWjeaKxZ_GiXcsFxJlThFJGO5QKDQxaTGojFHiVPumCoJ6YsYEOKPHdJJtU59rEqGOVWKQ/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1GIWqSkZNuXf_zg2CrESTkx8X0PW_gl1iao4QNgyhxPTCr3ZL5J71TSbomlWf7Vy722LMZLcaKu37Y6DpAJj59r-v1fJwe86US5FvwPWVjizzB87BvqB0O6BixNXiqYBZmb8f6rAlj-3FeyYr8KFHgvNlFnwZz8t9WQ_sh0NLiBTM8o8Mr580kDzMeDrjbfRqNcSxVZytpDkyQPMOvWjeaKxZ_GiXcsFxJlThFJGO5QKDQxaTGojFHiVPumCoJ6YsYEOKPHdJJtU59rEqGOVWKQ/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/16aQO8xVCG6xpoPuePtpI-E8fhoVXzQdPI2wOBj3wYNzgDUAPaZVG-nZmrx1Jya958ldN2LYRqfRnrVYSuN9xGwx65eKX418eT9Jad0o6ik2418OzsvSk8jtkvqG7B82EDRLEnWXJx8v_vt5BsXXPQgb1k9msSUvStF58EYdmjtEnLgMIDaqdvokL32FC48__vbwdNodruTlt0-E83QJwSqQal32eJ2Ucu7iUZbQBgBoRlw2ilQAdBy_v41dd2Oa28mEVuk2wZmGmspCO6Tb_8g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
