Can you send the full text of the terminal output?
On 9/4/19 10:44 AM, Maxime Perron wrote:
External Email - Use CautionHi 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Greve, Douglas N.,Ph.D. DGREVE@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 CautionDear 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
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer