On Thu, Apr 24, 2008 at 1:24 PM, Kai Hwang <
khwang@cnbc.cmu.edu> wrote:
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
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