Re: [Freesurfer] Segmentation fault (core dumped) of freeview - Freesurfer

13 Oct 2021


      External Email - Use Caution
Hello Yuhui,
Did you try something like the following (from https://secure-web.cisco.com/1hub7Psr57JCR6YgoGWEJLmEuz6voF9O_4wwW1Ngq-Krek8...) to set FREESURFER_HOME (?) and then after source'ing the shell setup script you should of seen output like ...
$ export FREESURFER_HOME=/your_path_to/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME &nbsp; /home/tester/freesurferFSFAST_HOME &nbsp; &nbsp; &nbsp; /home/tester/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR &nbsp; &nbsp; &nbsp;/home/tester/freesurfer/subjectsMNI_DIR &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /home/tester/freesurfer/mni
$ which freeview/your_path_to/freesurfer/7.2.0/freeview
… set TUTORIAL_DATA …
I would try just typing freeview on the command line to test that it brings up an empty window before trying to run any of the tutorial commands with it,
$ freeview
- R.
On Oct 12, 2021, at 22:42, Yuhui LIANG 梁玉慧 &lt;liangyuhui@westlake.edu.cn&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello,As a beginner, I am trying to run freeview -v using tutorial_data by the code below.freeview -v \good_output/mri/T1.mgz \good_output/mri/wm.mgz \good_output/mri/brainmask.mgz \good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.white:edgecolor=blue \good_output/surf/lh.pial:edgecolor=red \good_output/surf/rh.white:edgecolor=blue \good_output/surf/rh.pial:edgecolor=red I am getting an error :Segmentation fault (core dumped)but it did not produce CORE file. And I've downloaded the&nbsp;tutorial data set&nbsp;before begin and I am sure that set the TUTORIAL_DATA environment variable properly as specified on the tutorial data page.
I am using freesurfer version 7.2.0 in CentOS 8.
Any advice would be appreciated!
Thanks,
Yuhui_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1Thxeq5mfyjHL_ecNgfklwIAfLQXmU16VfwPdyUKAEKqI3t...