{"push_id":2310303557,"size":13,"distinct_size":1,"ref":"refs/heads/master","head":"f64c37d7c58cda46c80abc475ea64724b2bce2c3","before":"02bc6485596d0b82956092f87bd0bd43b0a2ee44","commits":[{"sha":"5b7d1cdb16e4f666ce422b140ceed14ab3750e8f","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"Added expert options to recon-all -hires\n\nPer information here:\nhttps://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon added an\nexpert options file (hires_expert) called from run_recon_all.sh","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/5b7d1cdb16e4f666ce422b140ceed14ab3750e8f"},{"sha":"fa8794a905be2b8c3214fa4242ad9ed79835019a","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"parallelizing spatial_afni_proc\n\nadjusted input params to spatial_afni_proc_SEalign.sh so that\npreproc_RF (and, eventually, preproc_task) can use UNIX parallel too to\ncall multiple instances simultaneously. seems functional, not\naggressively tested yet","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/fa8794a905be2b8c3214fa4242ad9ed79835019a"},{"sha":"9c7311ec2d7e2e846a71c1b465c814723cb7d520","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"added soft link\n\nensure a soft link to freesurfer directory exists","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/9c7311ec2d7e2e846a71c1b465c814723cb7d520"},{"sha":"5beb3e76d42f18d27c141c16986b1fc9654eb554","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"[untested] updates to preproc_task.sh\n\nsimilar to preproc_RF.sh, parallelize call to\nspatial_afni_proc_SEalign.sh. Eventually need to save original # of\nthreads rather than defaulting all users to 24…","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/5beb3e76d42f18d27c141c16986b1fc9654eb554"},{"sha":"ebd7b5dcca7b3624107907f255f6ed2fb96841d8","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"fixed typo in opts file\n\nmris-inflate to mris_inflate…","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/ebd7b5dcca7b3624107907f255f6ed2fb96841d8"},{"sha":"9bd4c45b899d160e9ff6c79be6ad56dcc5a5e78e","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"updated to use commas as separators in _SEtargets.txt\n\nInstead of space/tab, we’ll just use commas to delineate the 3 columns\nin SUBJ_SESS_SEtargets.txt - seems to work ok, and easier to see if\ncorrect. Also small bug fix to preproc_task.sh which was incorrectly\nrunning spatial_afni_proc_SEalign.sh before the parallelized call","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/9bd4c45b899d160e9ff6c79be6ad56dcc5a5e78e"},{"sha":"57629ba753cd0aa2c706445343572a4364432c38","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"surf2vol added back to preproc_task.sh\n\nwas accidentally missing","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/57629ba753cd0aa2c706445343572a4364432c38"},{"sha":"adc09fc412f321c23f9b60e93393e13a7293785c","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"fix to preproc_task.sh\n\nfixed how motion files concatenated, and re-added code to create QC\nmovie","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/adc09fc412f321c23f9b60e93393e13a7293785c"},{"sha":"4c64d3af76ef9a3030839232dc30d741057d9802","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"only unwarp in PE direction\n\nIn our datasets, the PE direction corresponds to the ‘y’ dimension of\nAFNI images (RAI). So we no longer want to fit an unwarping field along\nall 3 dimensions - instead, just the dimension of maximal distortions.\nQualitatively, this seems to improve distortion correction, but haven’t\nquantified yet","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/4c64d3af76ef9a3030839232dc30d741057d9802"},{"sha":"26b5401d1b44d9d7ff5140a43c52042de06f4059","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"added substituteLines.sh\n\n(from MR; not implemented yet)","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/26b5401d1b44d9d7ff5140a43c52042de06f4059"},{"sha":"f16dc53fb3871657eaad3f58a8a2a36177c7f76a","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"added PE-only distortion correction to SEtarget images\n\nhad forgotten to include the new -blip_opts_qw flag in the SE image\nunwarping step - added now","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/f16dc53fb3871657eaad3f58a8a2a36177c7f76a"},{"sha":"fcc4c7a0c87b46f83d25bebcd6db2cee8c653100","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"Merge branch 'master' into parallelize_afni_proc","distinct":false,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/fcc4c7a0c87b46f83d25bebcd6db2cee8c653100"},{"sha":"f64c37d7c58cda46c80abc475ea64724b2bce2c3","author":{"name":"Tommy Sprague","email":"c072a4e78e6be3029a0cdf107780748c04b679ba@gmail.com"},"message":"Merge pull request #6 from tommysprague/parallelize_afni_proc\n\nParallelize afni proc","distinct":true,"url":"https://api.github.com/repos/tommysprague/preproc_shFiles/commits/f64c37d7c58cda46c80abc475ea64724b2bce2c3"}]}
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