On Tue, 2008-05-06 at 16:55 -0400, Kai Hwang wrote:
> Hello Doug,
> Yes fieldsign maps were created by paint-sess without any problem, I was
> able to view my fieldsign overlays with surf-sess in stable-3 version,
> but not version 4.
>
> Kai
>
>
> Doug Greve 提到:
> > Did paint-sess complete? Are there field sign maps created?
> >
> > Elif SIKOGLU wrote:
> >> Hello,
> >>
> >> I have the same surf-sess problem as Kai. First I see the inflated
> >> brain and then the view screen turns black and nothing shows up. It
> >> is only for fieldsign map. eccentricity and polar maps look good.
> >>
> >> Any suggestions?
> >>
> >> Thanks,
> >> Elif
> >>
> >> On Thu, Apr 24, 2008 at 1:24 PM, Kai Hwang <
khwang@cnbc.cmu.edu
> >> <mailto:
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
> >> <
http://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
> >> _______________________________________________
> >> Freesurfer mailing list
> >>
Freesurfer@nmr.mgh.harvard.edu
> >> <mailto:
Freesurfer@nmr.mgh.harvard.edu>
> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> ------------------------------------------------------------------------
> >>
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> >>
Freesurfer@nmr.mgh.harvard.edu
> >>
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> >
greve@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > In order to help us help you, please follow the steps in:
> >
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> >
> > ------------------------------------------------------------------------
> >
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> >
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