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:
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Good evening Greve,
Thanks for your quick answer.
I attached the file containing the output.
Best,
Maxime
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On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto: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:
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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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
de la part de Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Envoyé : 4 septembre 2019 10:37
À : freesurfer@nmr.mgh.harvard.edu<mailto: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:
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​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
​
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