External Email - Use Caution Good evening Greve,
Thanks for your quick answer. I attached the file containing the output. Best, Maxime
recon-all.log
Description: recon-all.log
> On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > wrote: > > Can you send the full text of the terminal output? > > On 9/4/19 10:44 AM, Maxime Perron wrote: >> External Email - Use Caution >> >> Hi Greve, >> >> The exact script is the following : >> ____ >> >> setenv SUBJECTS_DIR >> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data >> >> make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" >> "Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" >> "Freesurfer_S021" "Freesurfer_S023" "Freesurfer_S024" "Freesurfer_S027" >> "Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" >> "Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" >> "Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" >> "Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" >> "Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" >> "Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" >> "Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" >> "Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" >> "Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" >> "Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" >> "Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" >> "Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" >> "Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" >> "Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" >> "Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" >> "Freesurfer_S158" "Freesurfer_S164" --out BrainaverageN72 >> >> cd >> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72 >> mkdir ori >> >> cd >> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72 >> @SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72 >> >> _____ >> >> BrainaverageN72 is the output name. >> >> Thanks, >> Maxime Perron >> ________________________________________ >> De : freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Greve, Douglas >> N.,Ph.D. <dgr...@mgh.harvard.edu> >> Envoyé : 4 septembre 2019 10:37 >> à : freesurfer@nmr.mgh.harvard.edu >> Objet : Re: [Freesurfer] make_average_subject error >> >> Is BrainaverageN72 in the subjects list? >> >> On 9/3/19 12:39 PM, Maxime Perron wrote: >>> External Email - Use Caution >>> >>> âDear Freesurfer Experts, >>> >>> >>> I have the following issue when running the make_average_subject command ( >>> >>> make_average_subject --subjects (Subjid) --out BrainaverageN72) : >>> >>> >>> Building hash of lh white >>> >>> Building hash of lh pial >>> >>> Building hash of rh white >>> >>> Building hash of rh pial >>> >>> Loading aseg from >>> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz >>> ASeg Vox2RAS: ----------- >>> -1.00000 0.00000 0.00000 128.00000; >>> 0.00000 0.00000 1.00000 -128.00000; >>> 0.00000 -1.00000 0.00000 128.00000; >>> 0.00000 0.00000 0.00000 1.00000; >>> mghRead(mri/norm.mgz, -1): could not open file >>> ------------------------- >>> >>> Labeling Slice >>> relabeling unlikely voxels in interior of white matter >>> Segmentation fault >>> Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun >>> Jun 2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64 >>> >>> recon-all -s BrainaverageN72 exited with ERRORS at Tue Sep 3 11:33:02 >>> EDT 2019 >>> >>> >>> I appreciate any help. >>> >>> âRegards, >>> Maxime >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> â >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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