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Support for compiling FreeSurfer from source #445

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Support for compiling FreeSurfer from source #445

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Commits on Feb 26, 2021

  1. [WIP] working in freesurfer from source

    @pwighton
    pwighton committed Feb 26, 2021
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  2. [WIP] trying to port mcr template

    @pwighton
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  3. [WIP] env vars for fs from source

    @pwighton
    pwighton committed Feb 26, 2021
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  4. [WIP] tweaks

    @pwighton
    pwighton committed Feb 26, 2021
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Commits on Mar 2, 2021

  1. [WIP] up to make install

    @pwighton
    pwighton committed Mar 2, 2021
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Commits on Mar 4, 2021

  1. [WIP] having issues with git annex

    @pwighton
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  2. [WIP] working verison?

    @pwighton
    pwighton committed Mar 4, 2021
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  3. [FIX] tweaks

    @pwighton
    pwighton committed Mar 4, 2021
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  4. [WIP] this builds fs

    @pwighton
    pwighton committed Mar 4, 2021
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  5. [WIP] a lot more params

    @pwighton
    pwighton committed Mar 4, 2021
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  6. [FIX] tweaks

    @pwighton
    pwighton committed Mar 4, 2021
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Commits on Mar 5, 2021

  1. [WIP] working on infant stream from source

    @pwighton
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Commits on Apr 27, 2021

  1. [FIX] installs python reqs

    @pwighton
    pwighton committed Apr 27, 2021
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  2. [FIX] typo

    @pwighton
    pwighton committed Apr 27, 2021
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Commits on May 3, 2021

  1. [WIP] aws buildspec

    @pwighton
    pwighton committed May 3, 2021
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  2. [WIP] fix

    @pwighton
    pwighton committed May 3, 2021
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  3. [WIP] fix

    @pwighton
    pwighton committed May 3, 2021
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Commits on May 7, 2021

  1. [FIX] wrap around martinos specific niftireg install

    @pwighton
    pwighton committed May 7, 2021
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  2. [FIX] var rename

    @pwighton
    pwighton committed May 7, 2021
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  3. [WIP] adding unzip

    @pwighton
    pwighton committed May 7, 2021
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Commits on May 11, 2021

  1. [FIX] upgrating fs python env to 3.6.8

    @pwighton
    pwighton committed May 11, 2021
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Commits on May 13, 2021

  1. [GIT] manual merge

    @pwighton
    pwighton committed May 13, 2021
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  2. [WIP] install python env for non infant stream

    @pwighton
    pwighton committed May 13, 2021
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  3. [WIP] re-arrange cause git annex is slow

    @pwighton
    pwighton committed May 13, 2021
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  4. [WIP] debug echos

    @pwighton
    pwighton committed May 13, 2021
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Commits on May 20, 2021

  1. [FIX] bash bugfix

    @pwighton
    pwighton committed May 20, 2021
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  2. [WIP]

    @pwighton
    pwighton committed May 20, 2021
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  3. [WIP] syntax

    @pwighton
    pwighton committed May 20, 2021
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Commits on May 26, 2021

  1. [FIX] to support samseg vis

    @pwighton
    pwighton committed May 26, 2021
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Commits on Jun 8, 2021

  1. [WIP] to support samseg atlas building utils

    @pwighton
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  2. [WIP] re-arrange

    @pwighton
    pwighton committed Jun 8, 2021
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  3. [WIP] samseg atlas utils

    @pwighton
    pwighton committed Jun 8, 2021
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Commits on Jun 15, 2021

  1. [FIX] unlocking git annex before make install

    @pwighton
    pwighton committed Jun 15, 2021
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Commits on Jun 23, 2021

  1. [WIP] using -DGEMS_BUILD_EXECUTABLES to build samseg atlas tools

    @pwighton
    pwighton committed Jun 23, 2021
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  2. [WIP] test..

    @pwighton
    pwighton committed Jun 23, 2021
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Commits on Jul 2, 2021

  1. [FIX] moving default fs pkg dir, so /tmp can safely be removed

    @pwighton
    pwighton committed Jul 2, 2021
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Commits on Jul 7, 2021

  1. [FIX] adds pythonpath env var for fs packages

    @pwighton
    pwighton committed Jul 7, 2021
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Commits on Jul 13, 2021

  1. [WIP] the beginnings of dev options

    @pwighton
    pwighton committed Jul 13, 2021
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  2. [FIX] fs path stomp fix

    @pwighton
    pwighton committed Jul 13, 2021
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  3. [FIX] path stomp bug take 2: electric boogaloo

    @pwighton
    pwighton committed Jul 13, 2021
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Commits on Aug 11, 2021

  1. [WIP] tweaks for jupyter

    @pwighton
    pwighton committed Aug 11, 2021
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  2. Merge branch 'master' into 20210513-fs-source-and-infant-merge

    @pwighton
    pwighton committed Aug 11, 2021
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Commits on Aug 13, 2021

  1. [WIP] prereqs for jupyter

    @pwighton
    pwighton committed Aug 13, 2021
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  2. [WIP] New Params 

    - git_annex_get: "ON"
- dev_tools: "OFF"
- cxx_flags: "-msse2 -mfpmath=sse -fPIC -fpermissive"
- c_flags: "-msse2 -mfpmath=sse -fPIC -fpermissive"
- `make install` not run if `git_annex_get` is `OFF`.
- `make install` will run in the gems dir if `samseg_atlas_build` is `ON`
  - even if `git_annex_get` is `OFF`
    @pwighton
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Commits on Aug 25, 2021

  1. [WIP] refactor to use jinja conditionals

    @pwighton
    pwighton committed Aug 25, 2021
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Commits on Aug 26, 2021

  1. [FIX] syntax

    @pwighton
    pwighton committed Aug 26, 2021
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  2. [WIP] test

    @pwighton
    pwighton committed Aug 26, 2021
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  3. [WIP] debug

    @pwighton
    pwighton committed Aug 26, 2021
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Commits on Aug 27, 2021

  1. [WIP] adding license stuff back

    @pwighton
    pwighton committed Aug 27, 2021
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Commits on Aug 31, 2021

  1. [FIX]

    @pwighton
    pwighton committed Aug 31, 2021
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Commits on Sep 8, 2021

  1. [FIX] formatting

    @pwighton
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  2. [FIX] formatting

    @pwighton
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  3. [WIP] syntax text

    @pwighton
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  4. [WIP] test

    @pwighton
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  5. [WIP] test

    @pwighton
    pwighton committed Sep 8, 2021
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  6. [FIX] wip

    @pwighton
    pwighton committed Sep 8, 2021
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  7. [FIX] wip

    @pwighton
    pwighton committed Sep 8, 2021
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Commits on Sep 9, 2021

  1. [WIP] adding awscli as a dev tool (prolly not the best palce)

    @pwighton
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Commits on Sep 10, 2021

  1. [WIP] updating mni envs

    @pwighton
    pwighton committed Sep 10, 2021
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Commits on Sep 22, 2021

  1. [WIP] adding the ability to select indv commit

    @pwighton
    pwighton committed Sep 22, 2021
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  2. [FIX] dropping --single-branch from git clone

    @pwighton
    pwighton committed Sep 22, 2021
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Commits on Sep 23, 2021

  1. [WIP] test..

    @pwighton
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  2. [WIP] full test

    @pwighton
    pwighton committed Sep 23, 2021
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  3. [WIP] syntax test

    @pwighton
    pwighton committed Sep 23, 2021
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Commits on Sep 24, 2021

  1. [FIX] adding back matlabmcr

    @pwighton
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Commits on Oct 15, 2021

  1. [FIX] applying @kaczmarj's diff

    @pwighton
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  2. [FIX] merging matlabmcr

    @pwighton
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Commits on Oct 16, 2021

  1. [WIP] infant tensorflow fix

    @pwighton
    pwighton committed Oct 16, 2021
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Commits on Oct 18, 2021

  1. [WIP] not installing extra reqs with dev tools

    @pwighton
    pwighton committed Oct 18, 2021
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Commits on Nov 5, 2021

  1. [WIP] tweaks for singularity

    @pwighton
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Commits on Nov 16, 2021

  1. [FIX] moving from /tmp to /stage for singularity

    @pwighton
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Commits on Nov 17, 2021

  1. [WIP] changing fs source dir to /stage and symlinking infant aws entr… 

    …ypoint to /bin
    @pwighton
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Commits on Nov 23, 2021

  1. [WIP] merging in support for fs720

    @pwighton
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Commits on Feb 15, 2022

  1. [WIP] trying to support deb and rpm installations

    @pwighton
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  2. [DOC]

    @pwighton
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Commits on Mar 28, 2022

  1. [WIP] infant model inside container

    @pwighton
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Commits on Mar 29, 2022

  1. [WIP] copying the infant model into the container, but not by default

    @pwighton
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Commits on Apr 8, 2022

  1. [FIX] syntax tweak

    @pwighton
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  2. [WIP] syntax tweak

    @pwighton
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  3. [WIP] syntax tweak

    @pwighton
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Commits on Apr 11, 2022

  1. [FIX] syntax

    @pwighton
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Commits on Apr 12, 2022

  1. [WIP]

    @pwighton
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  2. [WIP]

    @pwighton
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Commits on Apr 13, 2022

  1. [FIX] defining SSCNN_MODEL_DIR

    @pwighton
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  2. [FIX] defining SSCNN_MODEL_DIR

    @pwighton
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Commits on Apr 14, 2022

  1. [ENH] making branch optional

    @pwighton
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  2. Merge branch 'master' into 20220414-fs-source

    @pwighton
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  3. [GIT] removing buildspec before PR

    @pwighton
    pwighton committed Apr 14, 2022
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Commits on Jun 9, 2022

  1. [FIX] remove whitespace

    @pwighton
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  2. [WIP] adding back buildspec

    @pwighton
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  3. [WIP] syntax tweak to support commit param

    @pwighton
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  4. [GIT] removing buildspec before pushing upstream

    @pwighton
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Commits on Jun 10, 2022

  1. [WIP] updating fs python to 3.6.8

    @pwighton
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Commits on Aug 3, 2022

  1. [FIX] fix for issue ReproNim#449

    @pwighton
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Commits on Aug 22, 2022

  1. Merge branch 'master' of github.com:ReproNim/neurodocker

    @pwighton
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Commits on Oct 21, 2023

  1. Merge pull request #1 from ReproNim/master 

    Updating master branch reflect ReproNim HEAD
    Patrick D. Lloyd authored Oct 21, 2023
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  2. Bringing Freesurfer-from-source up to date with master branch

    Patrick D. Lloyd committed Oct 21, 2023
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Commits on Oct 23, 2023

  1. Merge pull request #1 from Alafia-Ai/20220414-fs-source 

    Brings 20220414-fs-source branch up to date with ReproNim/master
    @pwighton
    pwighton authored Oct 23, 2023
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