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
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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
also check that tksurfer works on your platform. you should be able to run:
tksurfer bert lh inflated
and load a curv file and an overlay (like lh.thickness).
On Tue, 2008-05-06 at 16:42 -0400, Doug Greve wrote:
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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Kai,
If you're using the centos4 x86_64 build of freesurfer, try using this tksurfer:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64
cp tksurfer.bin $FREESURFER_HOME/bin chmod a+x $FREESURFER_HOME/bin/tksurfer.bin
Nick
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick, I am not using centos4 x86_64. I am using centos4.
Thanks, Elif
On Tue, May 6, 2008 at 5:04 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Kai,
If you're using the centos4 x86_64 build of freesurfer, try using this tksurfer:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64
cp tksurfer.bin $FREESURFER_HOME/bin chmod a+x $FREESURFER_HOME/bin/tksurfer.bin
Nick
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 getregion
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 showedup.
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Nick, Actually I'm using CentOS 4 not _x86_64. Kai
Nick Schmansky 提到:
Kai,
If you're using the centos4 x86_64 build of freesurfer, try using this tksurfer:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64
cp tksurfer.bin $FREESURFER_HOME/bin chmod a+x $FREESURFER_HOME/bin/tksurfer.bin
Nick
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, sorry for the delay. I've verified the problem with my data here, though the solution may take a while to find. As a temporary fix, I've written a matlab script which will conver the field sign map into something that can be loaded as a simple overlay (attached). Instructions for use are below.
doug
help convert_fieldsign err = convert_fieldsign(infname,outfname)
Loads a field sign (infname) as saved by the void write_fieldsign() in tksurfer and saves in the given output format. This allows the field sign map to be loaded as an overlay in tksurfer. This can also be used to convert a field sign mask.
Eg: In matlab: convert_fieldsign('fieldsign-lh','lh.fieldsign.mgh'); convert_fieldsign('fieldsignmask-lh','lh.fieldsignmask.mgh'); In the unix shell: mri_mask lh.fieldsign.mgh lh.fieldsignmask.mgh lh.fieldsign-masked.mgh tksurfer subjectname lh inflated \ -overlay lh.fieldsign-masked.mgh -fthresh 0.5
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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