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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-o31...; http://secure-web.cisco.com/1YdALusv0t23JR3fYBLLwG3oCI0mqdrqdgc2lSNI9nb8_fmA... +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_Nw...

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_Nw... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Bernardoni, Fabio Fabio.Bernardoni@uniklinikum-dresden.de Gesendet: Mittwoch, 30. Juni 2021 14:07:34 An: freesurfer mailing list Betreff: [Freesurfer] problem with mris_compute_lgi

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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-...; http://secure-web.cisco.com/1uAkOO7CtOzygpinM5tt9ZZHkhl_HV3HHZnI2wodEWKz8oNE... +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_gl1iao4QNgyhxPTCr3Z...

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_gl1iao4QNgyhxPTCr3Z... 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

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