what is your tksurfer command line? No wildcards or variables, just the command that you end up running
On 02/06/2017 03:34 PM, 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]), "snap_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 $env(SUBJECT_NAME) puts [trace vinfo lablpth] read_binary_curv puts "shittttttttt!!!, has bug here" I debug it and found that it can not really run this command: read_binary_curv, before, it can take some snapshots and save it to be rgb format, and i will also give you the output from the terminal:
*/Successfully parsed tksurfer.tcl/* */shitaaaaa/* *//Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/* */sub-PREVDEMALS0010001BE_ses-M0/* */ /* */subject is sub-PREVDEMALS0010001BE_ses-M0/* */hemi is lh/* */surface is inflated/* */surfer: current subjects dir: /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/* */surfer: not in "scripts" dir ==> using cwd for session root/* */surfer: session root data dir ($session) set to:/* */surfer: /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-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/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0)/* */Reading /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_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/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_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
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