Lei,
You have found a bug! Here is the fix:
With a text editor, open this file:
$FREESURFER_HOME/fsfast/bin/surf-sess
and replace these lines (line #s 374-378):
if(! $rtopy) then set tclcmd0 = twocond-flat.tcl else set tclcmd0 = $rtopymode-flat.tcl endif
with this text:
if(! $rtopy) then set tclcmd0 = $FREESURFER_HOME/lib/tcl/twocond-flat.tcl else set tclcmd0 = $FREESURFER_HOME/lib/tcl/$rtopymode-flat.tcl endif
and save the file.
I think surf-sess should then work. If you prefer, I've also attached the fixed file if you just want to copy it to $FREESURFER_HOME/fsfast/bin.
Nick
On Sat, 2006-09-09 at 11:47 +0200, Lei.Zhang@uniklinik-freiburg.de wrote:
Hi, dear Freesurfer,
I'm tring to analyse my retinotopic data with the new freesurfer version (freesurfer-Linux-centos4-stable-pub-v3.0.3-full.tar.gz) under Suse Linux10.1.
I follewed the processing step of FsFastIndividualRetinotopyAnalysis on your freesurferwiki, and now when I run the last step 'surf-sess -s sessid -a rtopy -c polar -flat', I got the errors, not only for polar, eccen, fieldsign and twocond-flat.tcl which I tried were the same result---'couldn't read file "***.tcl": no such file or directory'. I checked the folder and I can find these files. How can I do next?
Thanks for your help!
***Error message*** Session: RM07_retino ---- ------ lh hemisphere ------ /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal
/home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal tksurfer -RM07 lh inflated -tcl fs-flat.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal surfer: Reading header info from /usr/local/freesurfer/subjects/RM07/mri/T1.mgz surfer: vertices=165187, faces=330370 surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl tksurfer: run tcl script: fs-flat.tcl couldn't read file "fs-flat.tcl": no such file or directory%
Session: RM07_retino ---- ------ lh hemisphere ------ /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal
/home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal tksurfer -RM07 lh inflated -tcl eccen-flat.tcl
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 surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal surfer: Reading header info from /usr/local/freesurfer/subjects/RM07/mri/T1.mgz surfer: vertices=165187, faces=330370 surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl tksurfer: run tcl script: eccen-flat.tcl couldn't read file "eccen-flat.tcl": no such file or directory%
Lei Zhang Universitätsklinikum Freiburg Dept. of Diagnostic Radiology Medical Physics Hugstetter Strasse 55 79106 Freiburg, Germany
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