can you use freeview instead? The -help text is pretty extensive and
includes information on saving snapshots with -ss
cheers
Bruce
On Mon, 6 Feb 2017, Hao
wen wrote:
Hello:
Anyone can help me?
________________________________________________________________________________________________________
De : Hao wen
Envoyé : dimanche 5 février 2017 10:28
À : freesurfer@nmr.mgh.harvard.edu
Objet : Problem with using tksurfer to take snap shot with .tcl
Hello: FS experts:
I am now integrating to use tksurfer to take snapshot from command line
automatically, and my command is
like this:
```
cmd = "tksurfer %s %s inflated -tcl %s" % (subject, hemi,
os.path.join(os.path.dirname(sys.argv[0]), "sn
ap_tksurfer.tcl"))
```
so i use -tcl to define the behavior of tksurfer, but I go t a bug inside the
tickle script,
##curv
puts "shitaaaaa"
puts stdout [pwd]
puts stdout $env(SUBJECT_NAME)
puts [trace vinfo lablpth]
read_binary_curv
puts "shittttttttt!!!, has bug here"
I debug it and found that it can not really run this command: read_binary_curv,
before, it can take some
snapshots and save it to be rgb format, and i will also give you the output
from the terminal:
Successfully parsed tksurfer.tcl
shitaaaaa
/Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analys
is-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional
sub-PREVDEMALS0010001BE_ses-M0
subject is sub-PREVDEMALS0010001BE_ses-M0
hemi is lh
surface is inflated
surfer: current subjects
dir:/Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analys
is-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:
/Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analys
is-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional
checking for nofix files in 'inflated'
Reading image
info(/Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analy
sis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS
0010001BE_ses-M0)
Reading/Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analys
is-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0
010001BE_ses-M0/mri/orig.mgz
surfer: Reading header info
from/Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analys
is-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0
010001BE_ses-M0/mri/orig.mgz
surfer: vertices=98465, faces=196926
surfer: single buffered window
surfer: tkoInitWindow(sub-PREVDEMALS0010001BE_ses-M0)
setting percentile thresholds (-1.00, 0.00, 0.00)
surfer: using interface /Applications/freesurfer/tktools/tksurfer.tcl
tksurfer: run tcl script:
/Users/junhao.wen/Hao/Project/clinica_realted/CAPS_qa_clinica/snap_tksurfer.tcl
Reading /Applications/freesurfer/tktools/tkm_common.tcl
Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl
Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /Applications/freesurfer/tktools/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
I will also attach you the tcl file, any suggestion will be appreciated:)
PS: I know that FS right now recommand us to use freeview, do you have the
similar behavior like using
tcl file to define the behavior of freeview to take the snapshots???
Good day
Hao
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
