External Email - Use Caution I am not entirely sure :(
I did see someone else have the same exact issue and it says it was solved here: https://secure-web.cisco.com/1CITrHzRp2iUgFdotZPCjYwChbUZqcT7oSVSJaU_8J6xwEILhM4iXHWDVOXatRp-mQR2HIMUXdHX_dTFuyN7peCATDb-h7EBEbZap-khz2O0q7GmIB0zgfWDn66tSHJvtbaYIGkNhzFh8ZgpeIVjoXiSuglSZUixuQlYqhJOsgwQ2kPD1Tb-VpCrSYQA0pUX9VTSqAH4a0FvtyDAPCXRfpdwDElvAXMywq3bFaabMyHxwvEN0tLnqmFz5NN48zBeYvoVt09AEOczOMYCfv8W3p1mPYlrk6c9WXwT3f1o35RXO22QGjiEuCjOy0RR6NyhXQXId-bWTnRAEf9GLzM_Y2Q/https%3A%2F%2Fforum.freesurfer.net%2Ft%2Fpermission-denied-error-from-localgi%2F62 But when I try to click the link and sign up I don't receive any verification to my email (checked spam too). Not sure if anyone else can open it and view the solution? The recon -all finishes without error while using version 7.2.0, but when I run the following command: addpath('/usr/local/freesurfer_x86_64-7.2.0/matlab'); fsmri_pre_acpc = ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']); I get the next error: reading filled volume... /bin/bash: /scratch/tp44447785365264536.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp44447785365264536.load_mgh.m.mgh for reading And the scratch directory doesn't even exist. Best, Michael Ruvalcaba Knight Lab Helen Wills Neuroscience Institute University of California, Berkeley On Tue, Jan 9, 2024 at 8:25 PM fsbuild <fsbu...@contbay.com> wrote: > > Is SUBJECTS_DIR for Freesurfer being set to live under a temporary scratch > directory initially created by and then subsequently used by Matlab? > > If so, maybe Freesurfer is deleting files and/or changing file permissions > there - causing Matlab to subsequently complain. I would not expect > multiple programs writing to the same directory tree to work together if > they use different file permissions, privileges, and/or perform independent > clean/delete functions in shared directories. > > - R. > > On Jan 9, 2024, at 14:47, Michael Ruvalcaba <michaelruvalc...@berkeley.edu> > wrote: > > External Email - Use Caution > > Hello, > > I am trying to run the recon -all function in my MATLAB pipeline using > Freesurfer 6.0.0 and I have no issues with it. However, when I run the > recon -all step using Freesurfer 7.2.0 and run the following command (the > recon -all step finishes without error by the way): > > ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']); > > I get the following error: > > /bin/bash: /scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: > Permission denied > > The issue is there is no scratch file and it looks like between version > 6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch > directory (which 6.0.0 doesn't) > > Does anyone have any input on this? I hope this made sense! > > Best, > Michael Ruvalcaba > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1ChO_NcNoY9m6kgyc6Eqjwkz8Be1xpyj3-4TMeWFqLBMcQ1CCKoqORxcv7xcNplcFtsy-O0SEWB8CsVq0Lyi6LK17x9krLkQr047inFDLBslt0zgdLon1C_sG65-ofewngqMUl8KFBNXVODTu8tXem6yIPtqf-Nm5pbUZgJ-SrjO79tTI6beyJDV96PNSCNjiqddFzQ28qE74xFmGklvBWAUskaHO7TidfmaItYS6k4XjaJL175Ztpb_e-gi3SPNWsgL3baSnNSWCO6I6yFZP6USboGGktLA6HB1zR3_sVhHILJTon9QleO4suYGPeHZq6tIXuV_ZsiadPn7_jIe04w/https%3A%2F%2Fmail.nmr.mgh.harvard..edu%2Fmailman%2Flistinfo%2Ffreesurfer > > >
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