Don't use the -retinotopy flag. Look here
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
for more documentation on how to visualize the results
doug
On 12/05/2012 12:15 PM, Julia Foecker wrote:
sorry, there was a typo in the command line
this is the correct version:
tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE -retinotopy polar
Thanks, Julia
On Wed, 05 Dec 2012 11:01:43 -0500 Douglas N Greve greve@nmr.mgh.harvard.edu wrote
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 greve@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 greve@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 greve@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 greve@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@nmr.mgh.harvard.edu
-
Douglas N Greve