Good Morning, I have now been able to get the testing command: tksurfer bert rh pial to run, but it stops midway and issues a bus error. Please see the following script:
DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial subject is bert hemi is rh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/dbmuser checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) Bus error
Any idea what might be going wrong? I really need to use tksurfer to look at cortical thickness in gyrification in ROIs. (Oh and before I did this, I did set the environment as normal).
Thanks so much for your help! Claire
Daer Claire
The bus error might be related to Xquartz. Installing Xquartz again solved the issue on most Intel-based Macs.
Cheers Jürgen
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Von: Claire Morley clairemorley2014@u.northwestern.edu Antworten an: Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu Datum: Montag, 20. Oktober 2014 09:56 An: Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Bus error when trying to launch tksurfer
Good Morning, I have now been able to get the testing command: tksurfer bert rh pial to run, but it stops midway and issues a bus error. Please see the following script:
DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial subject is bert hemi is rh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/dbmuser checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) Bus error
Any idea what might be going wrong? I really need to use tksurfer to look at cortical thickness in gyrification in ROIs. (Oh and before I did this, I did set the environment as normal).
Thanks so much for your help! Claire
Hi Claire
what version are you using? And what is your hardware and software environment? RAM, OS version, etc....? Bruce On Mon, 20 Oct 2014, Claire Morley wrote:
Good Morning, I have now been able to get the testing command: tksurfer bert rh pial to run, but it stops midway and issues a bus error. Please see the following script:
DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial subject is bert hemi is rh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/dbmuser checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) Bus error
Any idea what might be going wrong? I really need to use tksurfer to look at cortical thickness in gyrification in ROIs. (Oh and before I did this, I did set the environment as normal).
Thanks so much for your help! Claire
--
We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Claire Morley -
Jürgen Hänggi