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davidmeunier79davidmeunier79
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Correc default params (#56)
* removed t1head_automask for marmo and marmot2 (marmot li threshold) * t1 gcc erode/diltate=6 for macaque * modif doc
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‎Dockerfile_spm_hdbet‎

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#
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# Timestamp: 2020/12/02 18:33:44 UTC
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FROM macatools/macapype:v0.5.10-full2
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FROM macatools/macapype:v0.6-spm-hdbet
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USER root
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‎Dockerfile_testpypi_spm_hdbet‎

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# Generated by: Neurodocker version 0.7.0+15.ga4940e3.dirty
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# Latest release: Neurodocker version 0.7.0
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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# pull request on our GitHub repository:
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#
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# https://github.com/ReproNim/neurodocker
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#
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# Timestamp: 2020/12/02 18:33:44 UTC
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FROM macatools/macapype:v0.6-spm-hdbet
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USER root
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ARG DEBIAN_FRONTEND="noninteractive"
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MAINTAINER David Meunier "david.meunier@univ-amu.fr"
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############################################# install skullTo3d
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RUN python -m pip install --no-deps --index-url https://test.pypi.org/simple/ --pre skullTo3d
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RUN python -c "import skullTo3d; print(skullTo3d.__version__)"

‎docs/command.rst‎

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*(but one is mandatory)*
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* ``-params`` : *(mandatory if -species is omitted)* a json file specifiying the global parameters of the analysis. See :ref:`Parameters <params>` for more details
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* ``-species`` : *(mandatory if -params is omitted)* followed the NHP species corresponding to the image, e.g. {macaque | marmo | baboon | chimp}
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* ``-species`` : *(mandatory if -params is omitted)* followed the NHP species corresponding to the image, e.g. {macaque | marmo }
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**NB** marmoT2 can be used for segmenting from the T2w image (by default, T1w is used for marmo)
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**NB** macaque_0p5 is available to use downsampled template (faster results)

‎docs/docker_install.rst‎

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Container install
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*****************
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Docker allows to provide all necessary softwares in extra to macapype packages. The Docker image we provide include ANTS 2.3.1, FSL 5.0.10 and AFNI (latest version). See at the bottom of this page for docker with SPM Stand-alone.
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Docker allows to provide all necessary softwares in extra to macapype packages. The Docker image we provide include ANTS 2.4.3, FSL 6.0.7.17 and AFNI (latest version). See at the bottom of this page for docker with SPM Stand-alone.
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**Note 1** :the image is quite big (~5GB) so requires some space on your "/" partition.
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**Note 2** : due to standard naming format, the repository on DockerHub is called "skullto3d", not "skullTo3d" - please note the difference in uppercase lowercase "T"...
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$ docker pull macatools/skullto3d:latest
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Starting from the release v0.2.1 on github, the docker images are tagged accordingly on Dockerhub:
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Docker images are tagged accordingly on Dockerhub:
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.. code:: bash
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$ docker pull macatools/skullto3d:version-0.2.1
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$ docker pull macatools/skullto3d:v0.1
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See :ref:`Quick test <quick_test>` for testing if your docker installation works properly on test datasets.
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**NB** for running ``-soft SPM`` and/or hdbet (corresponding ``-soft ANTS_quick``), a bigger version of the docker is available:
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.. code:: bash
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$ docker pull macatools/skullto3d:v0.1
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Note on Singularity
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-------------------
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.. code:: bash
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$ export SINGULARITY_TMPDIR=/tmp/; export SINGULARITY_CACHEDIR=/tmp/; sudo -E /path/to/bin/singularity build /path/to/containers/skullto3d_v0.0.4.1.sif docker://macatools/skullto3d:v0.0.4.1
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$ export SINGULARITY_TMPDIR=/tmp/; export SINGULARITY_CACHEDIR=/tmp/; sudo -E /path/to/bin/singularity build /path/to/containers/skullto3d_v0.1.sif docker://macatools/skullto3d:v0.1
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It *seems* the sudo priviliges are required to install and build images, so in case you have trouble, ask the admin of your cluster to perform this operation
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‎docs/quick_test.rst‎

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.. code:: bash
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$ singularity run -B /path/to/data:/data /path/to/containers/skullto3d_v0.0.5.sif segment_skull -data /data/skullTo3d_CI_v2/cerimed_marmo -out /data/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_skull_robustreg -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -padback
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$ singularity run -B /path/to/data:/data /path/to/containers/skullto3d_v0.1.sif segment_skull -data /data/skullTo3d_CI_v2/cerimed_marmo -out /data/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_skull_robustreg -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -padback
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Testing from docker image
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.. code:: bash
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$ docker run -v /path/to/data:/data macatools/skullto3d:v0.0.5 segment_skull -data /data/skullTo3d_CI_v2/cerimed_marmo -out /data/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_skull_robustreg -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -padback
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$ docker run -v /path/to/data:/data macatools/skullto3d:v0.1 segment_skull -data /data/skullTo3d_CI_v2/cerimed_marmo -out /data/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_skull_robustreg -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -padback
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Testing from python package install
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-----------------------------------
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.. code:: bash
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$ singularity run -B /path/to/data/:/data /path/to/containers/skullto3d_v0.0.5.sif segment_skull -data /data/skullTo3d_CI_v2/cerimed_macaque -out /data/skullTo3d_CI_v2/cerimed_macaque/results -soft ANTS_skull_robustreg -species macaque -sub Stevie -ses 01 -brain_dt T1 T2 -skull_dt CT petra t1 -deriv -padback
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$ singularity run -B /path/to/data/:/data /path/to/containers/skullto3d_v0.1.sif segment_skull -data /data/skullTo3d_CI_v2/cerimed_macaque -out /data/skullTo3d_CI_v2/cerimed_macaque/results -soft ANTS_skull_robustreg -species macaque -sub Stevie -ses 01 -brain_dt T1 T2 -skull_dt CT petra t1 -deriv -padback
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See :ref:`Commands <command>` for more info on robustreg in soft

‎workflows/params_segment_macaque_ants_4animal_skull.json‎

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"t1_skull_gcc_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 3.0
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"kernel_size": 6.0
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},
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"t1_skull_gcc_dilate":
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{
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"operation": "modal",
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"kernel_size": 3.0
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"kernel_size": 6.0
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},
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"t1_skull_dilate":
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‎workflows/params_segment_macaque_ants_4animal_skullnoisypetra.json‎

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"t1_skull_gcc_erode":
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‎workflows/params_segment_macaque_ants_quick_skull.json‎

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‎workflows/params_segment_macaque_ants_quick_skullnoisypetra.json‎

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‎workflows/params_segment_macaque_ants_skull.json‎

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{

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