New subject: Freeview on Mac not starting due PETSC error

15 Jun 2020


      External Email - Use Caution
Hello Alex,
While I'm (fsbuild) and not Ruopeng, I don't mind being mistaken for 
such a smart/nice guy ;-) .&nbsp; So I'm cc'ing back to the list so he and 
others can follow up.
It looks like you already have the commands to set FREESURFER_HOME and 
source the setup script in your $HOME/.bashrc file - as that information
 is printed out to the terminal after you run bash.&nbsp; So there should be 
no need to repeat typing those commands in the terminal window (though 
it should do no harm)..
I guess one question would be if it works for yo to do:
1) reboot your machine
2) start a new terminal window
3) type "bash"
.... see output from the freesurfer environment and then run the command ...
4) open -a $FREESURFER_HOME/Freeview.app
Then try loading a simple volume in freeview. (Under 
the freeview File pull down menu, select load volume, then you could try
 navigating to this file and select it, 
/Applications/freesurfer/7.1.0/subjects/bert/mri/brain.mgz - see screen 
shot below).
I think Ruopeng wanted to know if after the steps above, it also works 
for you to double click on Freeview.app in the Finder window and launch 
it (navigate with the Finder to /Applications/freesurfer/7.1.0).
You could try making bash your default shell with this command in the 
terminal window, so you don't have to type bash in step (3).
$ chsh -s /bin/bash
- R.
Alex White wrote:
Hello again Ruopeng,&nbsp;I copied those commands into my terminal. To my amazement, Freeview opened successfully with the command&nbsp;	open -a $FREESURFER_HOME/Freeview.appIt
 was also able to load a volume. And then I was able to start Freeview 
with the simpler command “freeview.” I can’t explain that.. The 
FREESURFER_HOME variable didn’t change, and my shell init script had 
already sourced SetUpFreesurfer.sh.&nbsp;However, I
 restarted my machine and tried again, and then Freeview wouldn’t open 
with either command, even following the whole sequence of commands you 
suggested. Then I tried again, and it worked. For some reason it’s only 
working intermittently.&nbsp;In response 
to your other question, when I double-clicked on the app bundle to start
 freeview, there was no crash report generated.Below is the output to the commands you requested. Do you see anything suspicious?&nbsp;Thanks a million!&nbsp;Alexalexlw@gse7359200 ~ % bash-------- freesurfer-darwin-macOS-7.1.0-20200511-813297b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME &nbsp; /Applications/freesurfer/7.1.0FSFAST_HOME &nbsp; &nbsp; &nbsp; /Applications/freesurfer/7.1.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR&nbsp; &nbsp; &nbsp; /Applications/freesurfer/7.1.0/subjectsMNI_DIR &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /Applications/freesurfer/7.1.0/mniThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://support.apple.com/kb/HT208050.bash-3.2$ sw_versProductName:	Mac OS XProductVersion:	10.15.5BuildVersion:	19F101bash-3.2$ echo $PATH | tr -s ':' '\n'/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/Users/alexlw/google-cloud-sdk/bin/Library/Frameworks/Python.framework/Versions/3.8/bin/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/alexlw/Library/Python/3.8/bin/Users/alexlw/Library/Python/3.8/bin/Users/alexlw/Library/Python/3.8/binbash-3.2$ ls /opt/X11/binX		bmtoa		font_cache	libpng-config	resize		x11perf		xditview	xfsinfo		xkeystone	xmore		xstdcmapXephyr		cvt		fonttosfnt	libpng16-config	sessreg		x11perfcomp	xdm		xgamma		xkill		xpr		xtermXfake		cxpm		freetype-config	listres		setxkbmap	xauth		xdmshell	xgc		xload		xprop		xvinfoXnest		editres		fslsfonts	lndir		showfont	xbacklight	xdpr		xhost		xlogo		xrandr		xwdXorg		fc-cache	fstobdf		luit		showrgb		xcalc		xdpyinfo	xinit		xlsatoms	xrdb		xwininfoXquartz		fc-cat		gccmakedep	makedepend	smproxy		xclipboard	xedit		xinput		xlsclients	xrefresh	xwudXvfb		fc-list		glxgears	mkfontdir	startx		xclock		xev		xkbbell		xlsfonts	xscopeappres		fc-match	glxinfo		mkfontscale	sxpm		xcmsdb		xeyes		xkbcomp		xmag		xsetatobm		fc-pattern	gtf		oclock		twm		xcompmgr	xfd		xkbevd		xman		xsetmodebdftopcf	fc-query	iceauth		png-fix-itxt	ucs2any		xconsole	xfindproxy	xkbprint	xmessage	xsetpointerbdftruncate	fc-scan		ico		pngfix		uxterm		xcursorgen	xfontsel	xkbvleds	xmh		xsetrootbitmap		fc-validate	koi8rxterm	quartz-wm	viewres		xcutsel		xfs		xkbwatch	xmodmap		xsm&nbsp;&nbsp;bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.0&nbsp;&nbsp;bash-3.2$ ls $FREESURFER_HOMEASegStatsLUT.txt		SetUpFreeSurfer.csh		diffusion			matlab				tkmeditParcColorsCMADefectLUT.txt			SetUpFreeSurfer.sh		docs				mni				trctrainFreeSurferColorLUT.txt		Simple_surface_labels2009.txt	etc				python				uninstall.shFreeSurferEnv.csh		WMParcStatsLUT.txt		fsafd				sessionsFreeSurferEnv.sh		average				fsfast				sources.cshFreeview.app			bin				lib				sources.shSegmentNoLUT.txt		build-stamp.txt			license.txt			subjects&nbsp;&nbsp;bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.1.0-20200511-813297b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME &nbsp; /Applications/freesurfer/7.1.0FSFAST_HOME &nbsp; &nbsp; &nbsp; /Applications/freesurfer/7.1.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR&nbsp; &nbsp; &nbsp; /Applications/freesurfer/7.1..0/subjectsMNI_DIR &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /Applications/freesurfer/7.1.0/mni&nbsp;bash-3.2$ echo $PATH | tr -s ':' '\n'/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/Users/alexlw/google-cloud-sdk/bin/Library/Frameworks/Python.framework/Versions/3.8/bin/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7..1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/alexlw/Library/Python/3.8/bin/Users/alexlw/Library/Python/3.8/bin/Users/alexlw/Library/Python/3.8/binbash-3.2$ open -a $FREESURFER_HOME/Freeview.app	Freeview opens…sometimes&nbsp;bash-3.2$ otool -L /Applications/freesurfer/7.1.0/Freeview.app/Contents/MacOS/freeview&nbsp;/Applications/freesurfer/7.1.0/Freeview.app/Contents/MacOS/freeview:	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 23.0.0)	/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0)	/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)	@rpath/QtWidgets.framework/Versions/5/QtWidgets (compatibility version 5.12.0, current version 5.12.7)	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.250.1)	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
 (compatibility version 1.0.0, current version 50.1.0)	/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 946.0.0)	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)	@rpath/QtGui.framework/Versions/5/QtGui (compatibility version 5.12.0, current version 5.12.7)	@rpath/QtCore.framework/Versions/5/QtCore (compatibility version 5.12.0, current version 5.12.7)	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.4)	/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit (compatibility version 45.0.0, current version 1671.60.107)	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
 (compatibility version 150.0.0, current version 1575.17.0)	/System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
 (compatibility version 64.0.0, current version 1265.9.0)	/System/Library/Frameworks/Foundation.framework/Versions/C/Foundation (compatibility version 300.0.0, current version 1575.17.0)	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)On Jun 14, 2020, at 8:49 PM, fsbuild &lt;fsbuild@contbay.com&gt; wrote:Hello Alex,See
 what you get for results on your Mac with the commands listed below. 
&nbsp;Your version of MacOS may be slightly different.&nbsp; It should work to cut
 and paste the commands below.- R.- - - - -&nbsp;buildqa-Mac:/tmp %&nbsp;bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://support.apple.com/kb/HT208050.buildqa-Mac:/tmp%3E%C2%A0sw_versProduc...:	Mac OS XProductVersion:	10.15.2BuildVersion:	19C57buildqa-Mac:/tmp&gt;&nbsp;echo $PATH | tr -s ':' '\n'&nbsp;/usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/buildqa/binbuildqa-Mac:/tmp&gt;&nbsp;ls /opt/X11/binX@&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;cvt*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;freetype-config* lndir*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;showrgb*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xclipboard*&nbsp; &nbsp; &nbsp;&nbsp;xev*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xkbcomp*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xman*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xsetpointer*Xephyr*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;cxpm*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fslsfonts*&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;luit*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;smproxy*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xclock*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xeyes*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xkbevd*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xmessage*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xsetroot*Xfake*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;editres*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fstobdf*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;makedepend*&nbsp; &nbsp; &nbsp;&nbsp;startx*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xcmsdb*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xfd*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xkbprint*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xmh*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xsm*Xnest*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fc-cache*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;gccmakedep*&nbsp; &nbsp; &nbsp;&nbsp;mkfontdir*&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;sxpm*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xcompmgr*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xfindproxy*&nbsp; &nbsp; &nbsp;&nbsp;xkbvleds*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xmodmap*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xstdcmap*Xorg*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fc-cat*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;glxgears*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;mkfontscale*&nbsp;&nbsp; &nbsp;&nbsp;twm*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xconsole*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xfontsel*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xkbwatch*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xmore*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xterm*Xquartz*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fc-list*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;glxinfo*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;oclock*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;ucs2any*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xcursorgen*&nbsp; &nbsp; &nbsp;&nbsp;xfs*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xkeystone*&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;xpr*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xvinfo*Xvfb*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fc-match*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;gtf*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;png-fix-itxt*&nbsp; &nbsp;&nbsp;uxterm*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xcutsel*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xfsinfo*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xkill*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xprop*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xwd*appres*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fc-pattern*&nbsp; &nbsp; &nbsp;&nbsp;iceauth*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;pngfix*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;viewres*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xditview*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xgamma*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xload*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xrandr*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xwininfo*atobm*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fc-query*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;ico*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;quartz-wm*&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;x11perf*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xdm*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xgc*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xlogo*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xrdb*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xwud*bdftopcf*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fc-scan*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;koi8rxterm*&nbsp; &nbsp; &nbsp;&nbsp;resize*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;x11perfcomp*&nbsp;&nbsp; &nbsp;&nbsp;xdmshell*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xhost*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xlsatoms*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xrefresh*bdftruncate*&nbsp;&nbsp; &nbsp;&nbsp;fc-validate*&nbsp;&nbsp; &nbsp;&nbsp;libpng-config@&nbsp;&nbsp;&nbsp;sessreg*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xauth*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xdpr*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xinit*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xlsclients*&nbsp; &nbsp; &nbsp;&nbsp;xscope*bitmap*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;font_cache*&nbsp; &nbsp; &nbsp;&nbsp;libpng16-config* setxkbmap*&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;xbacklight*&nbsp; &nbsp; &nbsp;&nbsp;xdpyinfo*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xinput*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xlsfonts*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xset*bmtoa*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fonttosfnt*&nbsp; &nbsp; &nbsp;&nbsp;listres*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;showfont*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xcalc*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xedit*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xkbbell*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xmag*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;xsetmode*buildqa-Mac:/tmp&gt;&nbsp;export FREESURFER_HOME=/Applications/freesurfer/7.1.0buildqa-Mac:/tmp&gt;&nbsp;ls $FREESURFER_HOMEASegStatsLUT.txt*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;SetUpFreeSurfer.sh*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;etc/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sources.csh*DefectLUT.txt*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;Simple_surface_labels2009.txt* fsafd/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sources.sh*FreeSurferColorLUT.txt*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;WMParcStatsLUT.txt*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fsfast/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;subjects/FreeSurferEnv.csh*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;average/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;lib/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;tkmeditParcColorsCMA*FreeSurferEnv.sh*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;bin/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;matlab/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;trctrain/Freeview.app/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;build-stamp.txt*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;mni/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;uninstall.sh*SegmentNoLUT.txt*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;diffusion/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;python/SetUpFreeSurfer.csh*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;docs/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sessions/buildqa-Mac:/tmp&gt;&nbsp;source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.1.0-20200511-813297b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME&nbsp;&nbsp;&nbsp;/Applications/freesurfer/7.1.0FSFAST_HOME&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.1.0/fsfastFSF_OUTPUT_FORMAT nii..gzSUBJECTS_DIR&nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.1.0/subjectsMNI_DIR&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.1.0/mnibuildqa-Mac:/tmp&gt;&nbsp;echo $PATH | tr -s ':' '\n'/Applications/freesurfer/7.1.0/bin/Applications/freesurfer/7.1.0/fsfast/bin/Applications/freesurfer/7.1.0/mni/bin/usr/local/bin/usr/bin/bin/usr/sbin/sbin/opt/X11/bin/Users/buildqa/binbuildqa-Mac:/tmp&gt;&nbsp;open -a $FREESURFER_HOME/Freeview.app&lt;...pop
 up window asking to accept network connections, then freeview should 
open in a separate window … then exit freeview...&gt;buildqa-Mac:/tmp&gt;&nbsp;otool -L /Applications/freesurfer/7.1.0/Freeview.app/Contents/MacOS/freeview&nbsp;/Applications/freesurfer/7.1.0/Freeview.app/Contents/MacOS/freeview:	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 23.0.0)	/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0)	/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)	@rpath/QtWidgets.framework/Versions/5/QtWidgets (compatibility version 5.12.0, current version 5.12..7)	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.250.1)	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
 (compatibility version 1.0.0, current version 50.1.0)	/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 946.0.0)	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)	@rpath/QtGui.framework/Versions/5/QtGui (compatibility version 5.12.0, current version 5.12.7)	@rpath/QtCore.framework/Versions/5/QtCore (compatibility version 5.12.0, current version 5.12.7)	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.4)	/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit (compatibility version 45.0.0, current version 1671.60.107)	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
 (compatibility version 150.0.0, current version 1575.17.0)	/System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
 (compatibility version 64.0.0, current version 1265.9..0)	/System/Library/Frameworks/Foundation.framework/Versions/C/Foundation (compatibility version 300.0.0, current version 1575.17.0)	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)On Jun 14, 2020, at 18:34, fsbuild &lt;fsbuild@contbay.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello Alex,Did you try the install with the 7.1.0 release using the .pkg file installer from&nbsp;https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darw...
 you did not go thru all the security exemptions (not related to your 
firewall settings) on Catalina, then something may be blocked from 
running.&nbsp; The install procedure to follow using the .pkg installer is 
under,https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_macI did this on my mac running Catalina and had no issues running freeview..- R.On Jun 14, 2020, at 17:45, Alex White &lt;alexander.l.white@gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi Ruopeng&nbsp;I
 tried deleting that .plist file, but it did not work, even after 
restarting the machine. The same PETSC crash occurred when I try to 
start Freeview either through the terminal or clicking on the icon.&nbsp;Thanks for your continued help,&nbsp;AlexOn Jun 14, 2020, at 2:29 PM, Wang, Ruopeng &lt;RWANG4@mgh.harvard.edu&gt; wrote:Can you delete this file and wait for a minute and then try starting freeview again?/Users/USERNAME/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plistReplace USERNAME with your actual username.&nbsp;On Jun 14, 2020, at 1:47 PM, Alex White &lt;alexander.l.white@gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello&nbsp;Ruopeng,&nbsp;Thanks for the quick reply!&nbsp;I
 tried launching Freeview by double-clicking on the app icon, and I 
tried installing the latest build. The same crash occurs (full output 
copied again below.&nbsp;Also,
 I do have XQuartz 2.7.11 and it can run xeyes. And yes, FREESURFER_HOME
 and SetUpFreesurfer.sh both reference the current version 7.1.0. I 
didn’t see any LD_LIBRARY_PATH in my shell init file. Here’s what’s in 
my .bashrc file:&nbsp;% cat .bashrc#set freesurfer directories and set up scriptexport FREESURFER_HOME=/Applications/freesurfer/7.1.0export SUBJECTS_DIR=$FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.shAny other ideas?&nbsp;Thanks,&nbsp;AlexCrash output:&nbsp;&nbsp;~ % freeview[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see&nbsp;http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...: or try&nbsp;http://valgrind.org%C2%A0on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run&nbsp;[0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC
 ERROR: Petsc Release Version 2.3.3, Patch 16, Tue Sep 23 10:02:49 CDT 
2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a darwin15. named gse7359200..local by alexlw Sun Jun 14 10:46:00 2020[0]PETSC
 ERROR: Libraries linked from 
/autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2..3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC
 ERROR: Configure options --with-debugging=no --download-f-blas-lapack=0
 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 
--with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0On Jun 14, 2020, at 6:56 AM, Wang, Ruopeng &lt;RWANG4@mgh.harvard.edu&gt; wrote:HI Alex,Have you tried launching freeview by double-clicking freeview.app bundle?&nbsp;Can you also try the latest build from here?https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewBest,RuopengOn Jun 14, 2020, at 12:07 AM, Alex White &lt;alexander.l.white@gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello freesurfer team!&nbsp;I can’t get Freeview to start up on my Mac (Catalina v 10.15.15).&nbsp;It
 worked intermittently earlier this year, then stopped working. I 
updated Freeview, and then all of freesurfer, and still have the same 
problem. So now I have this version of freesurfer: 
&nbsp;freesurfer-darwin-macOS-7.1.0-20200511-813297bTyping “freeview” into the terminal generates the following error:&nbsp;[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see&nbsp;http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...: or try&nbsp;http://valgrind.org%C2%A0on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run&nbsp;[0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC
 ERROR: Petsc Release Version 2.3.3, Patch 16, Tue Sep 23 10:02:49 CDT 
2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a darwin15. named gse7359200.local by alexlw Sat Jun 13 20:58:43 2020[0]PETSC
 ERROR: Libraries linked from 
/autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2.3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC
 ERROR: Configure options --with-debugging=no --download-f-blas-lapack=0
 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 
--with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0I
 searched through the log of previous emails and found several others 
with “PETSC errors” but could not discern a common solution.&nbsp;Help?&nbsp;Thank you,&nbsp;Alex White&nbsp;PS: I also can’t get Freeview to launch on a linux machine, and will send a report on that in a separate email.&nbsp;_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "mail.nmr.mgh..harvard.edu" claiming to be&nbsp;https://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer_______________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freeview on Mac not starting due PETSC error