Have you looked at the modifications for the BIDS App version:

https://github.com/BIDS-Apps/freesurfer

I believe the latest image (using FS6) is only 6.37GB and you could bypass the run.py script with --entrypoint bash to run your typical recon-all commands

-Alex

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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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