Re: [Freesurfer] make_average_subject error

[Maxime Perron]

External Email - Use Caution         Hi Andrew, I am very sorry for the delay of my answer.  Everything works with the patch.  Thank you so much! Cheers, Maxime On Oct 10, 2019, at 11:39 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: Hi Maxine,   https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ contains executables and a README file that details how you can patch your freesurfer install to fix this issue.   best Andrew     From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@ulaval.ca> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu> Date: Friday, September 6, 2019 at 5:08 PM To: FS Help <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] make_average_subject error           External Email - Use Caution         ​Hi Douglas,    I'm sorry for the misunderstanding! Thanks for the command.   I attached the mas.log.    Cheers, Maxime  ​   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 : 6 septembre 2019 10:30 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] make_average_subject error   That is the recon-all.log file. What I want is the terminal output from make_average_subject You can capture it with  make_average_subject [your arguments] |& tee mas.log On 9/4/2019 9:16 PM, Maxime Perron wrote:         External Email - Use Caution          Good evening Greve,   Thanks for your quick answer.   I attached the file containing the output.   Best, Maxime _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer      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   ​Dear 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.   ​Regards, Maxime                   ​       _______________________________________________ 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 _______________________________________________ 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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