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Today's Topics:

   1. Problem with using tksurfer to take snap shot with .tcl (Hao wen)
   2. Slim down FS6 (Marmaduke Woodman)


---------- Forwarded message ----------
From: Hao wen <hao.freesurfer@hotmail.com>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: 
Date: Sun, 5 Feb 2017 09:28:19 +0000
Subject: [Freesurfer] 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

---------- Forwarded message ----------
From: Marmaduke Woodman <mmwoodman@gmail.com>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: 
Date: Sun, 5 Feb 2017 14:23:25 +0100
Subject: [Freesurfer] Slim down FS6
Hi

I'm using just the standard structural recon-all pipeline, nothing else. FS6's directory totals just over 9 GiB. Is there a way to slim that down, or is it all required for the structural pipeline?

I'm using Docker containers, hence trying to slim down the image size.

Thanks,
Marmaduke





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