Hello, I'm trying to use freesurfer to map the visual cortex and get region borders of V1, V2.. etc. We used a conventional rotating/expanding wedge paradigm, and I followed the steps described in FsFastIndividualRetinotopy Analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
Everything worked fine till the last step, I can't view the results with surf-sess. After I execute the command surf-sess, first a flatten cortex appeared, then the view screen turned black and nothing showed up.
Here is what I have in the terminal window
hwang@kaih:~/Subjects> surf-sess -s Pilot1 -a VM_retinotopy -retinotopy fieldsign -flat grep: /home/hwang/Subjects/Pilot1/session.info: No such file or directory ----------------------------------------------------------------- surf-sess logfile is /home/hwang/Subjects/log/surf-sess.VM_retinotopy.fs.log ----------------------------------------------------------------- ------------------------------------------------------ ------------------------------------------------------ Session: Pilot1 ---- ------ lh hemisphere ------ /home/hwang/Subjects/Pilot1/bold/VM_retinotopy ---------------------------------------------------------- /home/hwang/Subjects/Pilot1/bold/VM_retinotopy tksurfer -Pilot1 lh inflated -tcl /usr/local/freesurfer/lib/tcl/fs-flat.tcl ---------------------------------------------------------- Loading /usr/local/freesurfer/surface_labels.txt surfer: current subjects dir: /home/hwang/Subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/hwang/Subjects/Pilot1/bold/VM_retinotopy surfer: Reading header info from /home/hwang/Subjects/Pilot1/mri/T1.mgz surfer: vertices=149915, faces=299826 can't find talairach file '/home/hwang/Subjects/Pilot1/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: ### redraw failed: no gl window open Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... tksurfer: fs-flat.tcl: set flags setdefpatchview: ### position.tcl for Pilot1 does not exist setdefpatchview: ### setting flatzrot to 90 (default) setdefpatchview: ### setting flatscale to 1.0 (default) setdefpatchview: ### setting flatxtrans to 0.0 (default) setdefpatchview: ### setting flatytrans to 0.0 (default) readenv.tcl: ==> read global setenv vars readenv: set invphaseflag 0 readenv: set fm fieldsign/fieldsignmask-lh readenv: set angle_offset 0 readenv: set dir /home/hwang/Subjects/Pilot1/bold/VM_retinotopy 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 use_vertex_arrays 0 readenv: set nosave 0 readenv: set polardir polar readenv: set noexit readenv: set curv lh.curv readenv: set patchname occip.patch.flat readenv: set fslope 1.3 readenv: set colscale 0 readenv: set mc () { . /usr/share/mc/bin/mc-wrapper.sh } readenv: set smoothsteps 2 readenv: set revpolarflag 0 readenv.tcl: ==> read rgbname-specific setenv vars % tksurfer: fs-flat.tcl: read curvature surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl tksurfer: run tcl script: /usr/local/freesurfer/lib/tcl/fs-flat.tcl surfer: curvature read: min=-1.677210 max=1.267429 % tksurfer: fs-flat.tcl: read patch tksurfer: fs-flat.tcl: read fieldsign tksurfer: fs-flat.tcl: read fieldsign mask surfer: read_fieldsign(fieldsign/fieldsign-lh) surfer: mris->nvertices = 149915, vnum = 149915 surfer: read_fsmask(fieldsign/fieldsignmask-lh) % tksurfer: fs-flat.tcl: scale, position brain surfer: ### GL window already open: can't open second % tksurfer: fs-flat.tcl: save rgb's tksurfer: fs-flat.tcl: save rgb surfer: dipscale=0.000000 % tksurfer: fs-flat.tcl: nosave setenv'd => nothing will be saved invalid command name "dontsave_rgb_named"% surfer: dipscale=0.000000 % surfer: dipscale=0.000000
any suggestion how to make surf-sess work?
Thanks! Kai