Hi Julia, what is your command line when you give it the hemisphere? Also, when you run it, put "-debug" as the first argument and send me the terminal output. doug
On 12/05/2012 10:55 AM, Julia Foecker wrote: > Hi Doug, > > I tried now several things to use the tksurfer command but it does not seem to > work. > > > tksurfer-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE > -retinotopy polar > > > > when I run the command and just replace tksurfer, it is asking for the > hemisphere > > ERROR: no hemisphere specified > > > When I am specifying the hemisphere it does not find the command... > > I think the problem according to the colortables has been already posted in > the > forum, but I cannot see any reply to that. It has been mentioned under a > different topic though (see link below). > > Thanks a lot for any advices, > Julia > > > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-April/007556.html > > > > > > > > > > > > > > On Tue, 04 Dec 2012 12:00:50 -0500 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote > >> 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.i >>> nfo: 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/Anal >>> ysisPhase ---------------------------------------------------------- >>> >>> > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/Anal >>> ysisPhase 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/Anal >>> ysisPhase 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/Anal >>> ysisPhase 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/ > > -- 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
