Hi Julia, I meant tksurfer-sess (not surf-sess) doug
On 12/04/2012 05:39 AM, Julia Foecker wrote: > Hi Doug, > thanks for your reply. > > I got the following messages when running the > > > surf-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE > -retinotopy polar > > and there was also this kind of message: > > GL window already open: can't open second > % tksurfer: polar-views.tcl: save rgb's > saveviews.tcl: nosave setenv'd => nothing will be saved > invalid command name "dontsave_rgb_named"% surfer: dmin=0.2470, vno=45600, > > I am still not sure what I can do so that this issue will not occur. > Do you have another advice? > > Thanks! > > Julia > > > > > WARNING: No colortable found! > invalid command name "urfer/subjects]" > % invalid command name "WARNING:" > % invalid command name "WARNING:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name > "mrisReadTriangleFile(/Users/foecker/Documents/Data/FMRI/Freesurfer/subjects/VGP01/surf/lh.sphere.reg):" > % % invalid command name "mrisReadTriangleFile" > % % % % invalid command name "WARNING:" > % % e buffered window > surfer: tkoInitWindow(VGP01) > surfer: using interface > /Users/foecker/Documents/freesurfer4/lib/tcl/tksurfer.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_common.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_wrappers.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/fsgdfPlot.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > % > invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "Reading" > % invalid command name "Reading" > % invalid command name "Reading" > % invalid command name "Reading" > % invalid command name "Successfully" > % invalid command name "reading" > % invalid command name "%" > % > % exit > [4157-JF-MACPRO1:FMRI/Freesurfer/subjects] foecker% tksurfer > usage: tksurfer subject hemisphere surface [options] > > subject : a subject directory in the SUBJECTS_DIR path > hemipshere : rh or lh > surface : a surface file name relative to the subject's surf directory > > Options > > -title title : set window title to title. Def is subject name. > -reassign : resample labels onto surface (set vnos=-1) > -sdir <path> : sets the subjects directory path > -orig <suffix> : sets the orig suffix string > -sphere <suffix>:sets the sphere.reg suffix string > > -patch <filename> : load a patch > > -tcl <filename> : run a script > > -annotation <filename> : load an annotation > -aparc : set annotation to aparc.annot and use outline mode > -colortable <filename> : load a color table file > -labels-under : display labels under any overlay > -label-outline : draw labels as outlines > > -curv : automatically load ?h.curv > -gray : automatically load ?h.curv and make it gray > > -overlay <filename> : load an overlay volume > -overlay-reg <filename> : use a file for the overlay registration > -overlay-reg-find : look in the data directory for a register.dat > : file > -overlay-reg-identity : calculate an identity transform for > registration > -mni152reg : for use with average subject when overlay is mni152 > -zm : remove mean from overlays > -fslope <value> : set the overlay threshold slope value > -fmid <value> : set the overlay threshold midpoint value > -fthresh <value> : set the overlay threshold minimum value > -foffset <value> : set the overlay threshold offset value > -colscalebarflag <1|0> : display color scale bar > -colscaletext <1|0> : display text in color scale bar > -truncphaseflag <1|0> : truncate the overlay display > -revphaseflag <1|0> : reverse the overlay display > -invphaseflag <1|0> : invert the overlay display > > -timecourse <filename> : load an timecourse volume > -timecourse-reg <filename> : use a file for the timecourse > : registration > -timecourse-reg-find : look in the data directory for a > : register.dat file > -timecourse-reg-identity : calculate an identity transform for > : regisrtation > -timecourse-offset <filename> : load an timecourse offset volume > -timecourse-offset-reg-file <filename> : use a file for the timecourse offset > : registration > -timecourse-offset-reg-find : look in the data directory for a > : register.dat file > -timecourse-offset-reg-identity : calculate an identity transform for > : registration > > -delink : do not move tool window with image window > -scalebarflag <1|0> : display the scale bar > > [4157-JF-MACPRO1:FMRI/Freesurfer/subjects] foecker% tksurfer VGP01 lh > usage: tksurfer subject hemisphere surface [options] > > subject : a subject directory in the SUBJECTS_DIR path > hemipshere : rh or lh > surface : a surface file name relative to the subject's surf directory > > Options > > -title title : set window title to title. Def is subject name. > -reassign : resample labels onto surface (set vnos=-1) > -sdir <path> : sets the subjects directory path > -orig <suffix> : sets the orig suffix string > -sphere <suffix>:sets the sphere.reg suffix string > > -patch <filename> : load a patch > > -tcl <filename> : run a script > > -annotation <filename> : load an annotation > -aparc : set annotation to aparc.annot and use outline mode > -colortable <filename> : load a color table file > -labels-under : display labels under any overlay > -label-outline : draw labels as outlines > > -curv : automatically load ?h.curv > -gray : automatically load ?h.curv and make it gray > > -overlay <filename> : load an overlay volume > -overlay-reg <filename> : use a file for the overlay registration > -overlay-reg-find : look in the data directory for a register.dat > : file > -overlay-reg-identity : calculate an identity transform for > registration > -mni152reg : for use with average subject when overlay is mni152 > -zm : remove mean from overlays > -fslope <value> : set the overlay threshold slope value > -fmid <value> : set the overlay threshold midpoint value > -fthresh <value> : set the overlay threshold minimum value > -foffset <value> : set the overlay threshold offset value > -colscalebarflag <1|0> : display color scale bar > -colscaletext <1|0> : display text in color scale bar > -truncphaseflag <1|0> : truncate the overlay display > -revphaseflag <1|0> : reverse the overlay display > -invphaseflag <1|0> : invert the overlay display > > -timecourse <filename> : load an timecourse volume > -timecourse-reg <filename> : use a file for the timecourse > : registration > -timecourse-reg-find : look in the data directory for a > : register.dat file > -timecourse-reg-identity : calculate an identity transform for > : regisrtation > -timecourse-offset <filename> : load an timecourse offset volume > -timecourse-offset-reg-file <filename> : use a file for the timecourse offset > : registration > -timecourse-offset-reg-find : look in the data directory for a > : register.dat file > -timecourse-offset-reg-identity : calculate an identity transform for > : registration > > -delink : do not move tool window with image window > -scalebarflag <1|0> : display the scale bar > > [4157-JF-MACPRO1:FMRI/Freesurfer/subjects] foecker% cd > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709 > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% source > example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% source > example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% source > example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% > mkanalysis-sess.new > -analysis $ANALYSIS_PHASE -TR 3 -paradigm $PARADIGM_PHASE -designtype > retinotopy -fsd bold -runlistfile $RUNLIST_PHASE -tpef $TIMEEXCLUDEFILE > -funcstem fmcsm5 -ncycles 10 -motioncor -inorm -polyfit 2 -force > TIMEEXCLUDEFILE: Undefined variable. > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% source > example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% > source example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% surf-sess -s > $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE -retinotopy polar > grep: > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/session.info: > No such file or directory > ----------------------------------------------------------------- > surf-sess logfile is > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/log/surf-sess.AnalysisPhase.polar.log > ----------------------------------------------------------------- > ------------------------------------------------------ > ------------------------------------------------------ > Session: ssRet_200709 ---- > ------ lh hemisphere ------ > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/AnalysisPhase > ---------------------------------------------------------- > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/AnalysisPhase > tksurfer -ssRet lh inflated -tcl > /Users/foecker/Documents/freesurfer4/lib/tcl/polar-views.tcl > ---------------------------------------------------------- > > > WARNING: No colortable found! > > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_common.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_wrappers.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/fsgdfPlot.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > tksurfer: polar-views.tcl: read and smooth complex Fourier comp > readenv.tcl: ==> read global setenv vars > readenv: set invphaseflag 0 > readenv: set fm fieldsign/fieldsignmask-lh > readenv: set angle_offset 0 > readenv: set dir > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/AnalysisPhase > readenv: set truncphaseflag 0 > readenv: set offset 0.4 > readenv: set fmid 0.8 > readenv: set fs fieldsign/fieldsign-lh > readenv: set lat > readenv: set fthresh 0.4 > readenv: set complexname -imag > readenv: set realname -real > readenv: set eccendir eccen > readenv: set floatstem map > readenv: set hemi lh > readenv: set rgbname map > readenv: set nosave 0 > readenv: set polardir polar > readenv: set noexit > readenv: set curv lh.curv > readenv: set fslope 1.3 > readenv: set colscale 0 > readenv: set smoothsteps 2 > readenv: set revpolarflag 0 > readenv.tcl: ==> read rgbname-specific setenv vars > % > tksurfer: polar-views.tcl: read curvature > surfer: current subjects dir: > /Users/foecker/Documents/Data/FMRI/Freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/AnalysisPhase > surfer: Reading header info from > /Users/foecker/Documents/Data/FMRI/Freesurfer/subjects/ssRet/mri/T1.mgz > surfer: vertices=164063, faces=328122 > surfer: single buffered window > surfer: tkoInitWindow(ssRet) > surfer: using interface > /Users/foecker/Documents/freesurfer4/lib/tcl/tksurfer.tcl > tksurfer: run tcl script: > /Users/foecker/Documents/freesurfer4/lib/tcl/polar-views.tcl > surfer: curvature read: min=-2.397066 max=4.657806 > % tksurfer: polar-views.tcl: read and smooth complex Fourier comp > surfer: smooth_val(2) > . > % tksurfer: polar-views.tcl: read and smooth real Fourier comp > surfer: smooth_val(2) > . > % tksurfer: polar-views.tcl: scale, position brain > surfer: ### GL window already open: can't open second > % tksurfer: polar-views.tcl: save rgb's > saveviews.tcl: nosave setenv'd => nothing will be saved > invalid command name "dontsave_rgb_named"% surfer: dmin=0.2470, vno=45600, > x=-9.9884, y=-67.7758, z=36.6844 > % surfer: curv=0.129080, fs=0.000000 > % surfer: val=0.085000, val2=0.865853 > % surfer: amp=0.870015, angle=84.393272 deg (0.234426) > % surfer: vertex 45600 marked (curv=0.129080, stat=0.000000) > x = (-10.0, -67.8, 36.7), n = (-0.7, -0.2, 0.6). > surfer: dmin=0.2022, vno=38559, x=-26.1600, y=-82.6320, z=-31.2516 > % surfer: curv=0.134054, fs=0.000000 > % surfer: val=1.473643, val2=1.667543 > % surfer: amp=2.225382, angle=48.532295 deg (0.134812) > % surfer: vertex 38559 marked (curv=0.134054, stat=0.000000) > x = (-26.2, -82.6, -31.3), n = (-0.9, -0.5, 0.2). > surfer: dmin=0.0986, vno=10616, x=-2.0371, y=-118.3332, z=-47.3615 > % surfer: curv=0.209849, fs=0.000000 > % surfer: val=-0.040989, val2=2.940233 > % surfer: amp=2.940519, angle=90.798691 deg (0.252219) > % > > > > On Mon, 03 Dec 2012 15:38:54 -0500 Douglas Greve <gr...@nmr.mgh.harvard.edu> > wrote > >> Hi Julia, try using tksurfer-sess instead >> doug >> >> On 12/3/12 12:08 PM, Julia Foecker wrote: >>> Dear Doug, >>> I tried to run Freesurfer on polar angle mapping data (I do not have >>> anyeccentricity data). Therefore, I created fake runs (as it has been >>> suggested in the forum). When I try to run the following command to load >>> the maps on the surface, >>> >>> surf-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE >>> -retinotopy polar >>> >>> >>> I got the following error message: There seems to be an issue with the >>> colortables...I have seen a similar issue in the forum, but could not find >>> the answer to that question. Would you have any suggestions what I can do >>> in this case? Moreover, when the command was running I have also seen the >>> lines: > >>> >>> > MRISwriteValues(/Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/VGP01_ >>> 180112/bold/AnalysisPhase//eccen/map-imag-rh.w): val at vertex 30887 is not >>> finite > >>> >>> Not sure what this means. Would you have any advices? >>> Many thanks in advance! >>> >>> Julia >>> >>> >>> >>> >>> WARNING: No colortable found! >>> >>> Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_common.tcl >>> Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_wrappers.tcl >>> Reading /Users/foecker/Documents/freesurfer4/lib/tcl/fsgdfPlot.tcl >>> Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkUtils.tcl >>> Successfully parsed tksurfer.tcl >>> reading white matter vertex locations... >>> tksurfer: polar-views.tcl: read and smooth complex Fourier comp >>> readenv.tcl: ==> read global setenv vars >>> readenv: set invphaseflag 0 >>> readenv: set fm fieldsign/fieldsignmask-rh >>> readenv: set angle_offset 0 >>> readenv: set dir >>> >>> > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/VGP01_180112/bold/Anal >>> ysisPhase readenv: set truncphaseflag 0 >>> readenv: set offset 0.4 >>> readenv: set fmid 0.8 >>> readenv: set fs fieldsign/fieldsign-rh >>> readenv: set lat >>> readenv: set fthresh 0.4 >>> readenv: set complexname -imag >>> readenv: set realname -real >>> readenv: set eccendir eccen >>> readenv: set floatstem map >>> readenv: set hemi rh >>> readenv: set rgbname map >>> readenv: set nosave 0 >>> readenv: set polardir polar >>> readenv: set noexit >>> readenv: set curv rh.curv >>> readenv: set fslope 1.3 >>> readenv: set colscale 0 >>> readenv: set smoothsteps 2 >>> readenv: set revpolarflag 0 >>> readenv.tcl: ==> read rgbname-specific setenv vars >>> % >>> tksurfer: polar-views.tcl: read curvature >>> surfer: single buffered window >>> surfer: tkoInitWindow(VGP01) >>> surfer: using interface >>> /Users/foecker/Documents/freesurfer4/lib/tcl/tksurfer.tcl >>> tksurfer: run tcl script: >>> /Users/foecker/Documents/freesurfer4/lib/tcl/polar-views.tcl >>> surfer: curvature read: min=-2.640939 max=1.554826 >>> % tksurfer: polar-views.tcl: read and smooth complex Fourier comp >>> surfer: smooth_val(2) >>> . >>> % tksurfer: polar-views.tcl: read and smooth real Fourier comp >>> surfer: smooth_val(2) >>> . >>> % tksurfer: polar-views.tcl: scale, position brain >>> surfer: ### GL window already open: can't open second >>> % tksurfer: polar-views.tcl: save rgb's >>> saveviews.tcl: nosave setenv'd => nothing will be saved >>> invalid command name "dontsave_rgb_named"% >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine >> at http://www.partners.org/complianceline . If the e-mail was sent to you in >> error but does not contain patient information, please contact the sender and >> properly dispose of the e-mail. >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
