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ENH: restricts datalad download and 'Basic' notebooks to sub-01
1 parent ced8dc7 commit fb79469

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+85
-147
lines changed

‎Dockerfile

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@@ -5,7 +5,7 @@
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# pull request on our GitHub repository:
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# https://github.com/kaczmarj/neurodocker
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#
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# Timestamp: 2018-03-17 00:20:22
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# Timestamp: 2018-03-20 12:07:05
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FROM neurodebian:stretch-non-free
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@@ -142,7 +142,7 @@ RUN mkdir /output && chmod 777 /output && chmod a+s /output
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USER neuro
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# User-defined BASH instruction
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RUN bash -c "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips*"
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RUN bash -c "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*"
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COPY [".", "/home/neuro/nipype_tutorial"]
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@@ -241,7 +241,7 @@ RUN echo '{ \
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\n ], \
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\n [ \
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\n "run_bash", \
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\n "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips*" \
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\n "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*" \
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\n ], \
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\n [ \
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\n "copy", \
@@ -273,6 +273,6 @@ RUN echo '{ \
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\n ] \
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\n ] \
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\n ], \
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\n "generation_timestamp": "2018-03-17 00:20:22", \
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\n "generation_timestamp": "2018-03-20 12:07:05", \
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\n "neurodocker_version": "0.3.2" \
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\n}' > /neurodocker/neurodocker_specs.json

‎create_dockerfile.sh

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@@ -21,7 +21,7 @@ docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-
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--run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
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--run 'mkdir /output && chmod 777 /output && chmod a+s /output' \
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--user=neuro \
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--run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips*' \
24+
--run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*' \
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--copy . "/home/neuro/nipype_tutorial" \
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--user=root \
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--run 'chown -R neuro /home/neuro/nipype_tutorial' \

‎notebooks/basic_data_input.ipynb

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@@ -409,7 +409,7 @@
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"source": [
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"As you can see, now `anat` contains ten file paths, T1w images for all ten subject. \n",
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"\n",
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"As a side node, you could also use ``[]`` string formating for some simple cases, e.g. \n",
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"As a side node, you could also use ``[]`` string formating for some simple cases, e.g. for loading only subject 1 adn 2: \n",
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"\n",
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" 'sub-0[1,2]/ses-test/anat/sub-0[1,2]_ses-test_T1w.nii.gz'"
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]
@@ -622,7 +622,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎notebooks/basic_data_output.ipynb

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@@ -303,7 +303,7 @@
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"\n",
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"# Skullstrip process\n",
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"ex1_skullstrip = Node(BET(mask=True), name=\"ex1_skullstrip\")\n",
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"ex1_skullstrip.inputs.in_file = \"/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz\""
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"ex1_skullstrip.inputs.in_file = \"/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\""
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]
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},
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{
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎notebooks/basic_error_and_crashes.ipynb

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@@ -302,7 +302,7 @@
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"from nipype.pipeline.engine import Node\n",
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"\n",
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"files = ['/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz',\n",
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" '/data/ds000114/sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz']\n",
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" '/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz']\n",
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"\n",
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"gunzip = Node(Gunzip(), name='gunzip',)\n",
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"\n",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎notebooks/basic_interfaces_caching.ipynb

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@@ -62,8 +62,8 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"bet_mem(in_file=\"/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz\",\n",
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" out_file=\"/output/sub-02_T1w_brain.nii.gz\",\n",
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"bet_mem(in_file=\"/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\",\n",
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" out_file=\"/output/sub-01_T1w_brain.nii.gz\",\n",
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" mask=True)"
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]
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"bet_mem(in_file=\"/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz\",\n",
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" out_file=\"/output/sub-02_T1w_brain.nii.gz\",\n",
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"bet_mem(in_file=\"/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\",\n",
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" out_file=\"/output/sub-01_T1w_brain.nii.gz\",\n",
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" mask=True)"
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]
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},
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"outputs": [],
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"source": [
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"mem.clear_runs_since()\n",
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"bet_mem(in_file=\"/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz\",\n",
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" out_file=\"/output/sub-02_T1w_brain.nii.gz\",\n",
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"bet_mem(in_file=\"/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\",\n",
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" out_file=\"/output/sub-01_T1w_brain.nii.gz\",\n",
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" mask=True)"
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]
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎notebooks/basic_mapnodes.ipynb

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@@ -151,8 +151,9 @@
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"from nipype.interfaces.spm import Realign\n",
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"from nipype.pipeline.engine import Node, MapNode, Workflow\n",
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"\n",
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"# Here we specify a list of files (for this tutorial, we just add the same file twice)\n",
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"files = ['/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz',\n",
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" '/data/ds000114/sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz']\n",
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" '/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz']\n",
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"\n",
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"realign = Node(Realign(register_to_mean=True),\n",
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" name='motion_correction')"
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"metadata": {},
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"source": [
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"```bash\n",
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"TraitError: The 'in_file' trait of a GunzipInputSpec instance must be an existing file name, but a value of ['/data/ds102/sub-01/func/sub-01_task-flanker_run-1_bold.nii.gz', '/data/ds102/sub-01/func/sub-01_task-flanker_run-2_bold.nii.gz'] <type 'list'> was specified.\n",
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"TraitError: The 'in_file' trait of a GunzipInputSpec instance must be an existing file name, but a value of ['/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz', '/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz'] <class 'list'> was specified.\n",
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"```"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"solution2": "hidden",
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"solution2": "shown",
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"solution2_first": true
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},
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"source": [
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"outputs": [],
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"source": [
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{
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"cell_type": "markdown",
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"source": [
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"let's print all nodes:"
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"outputs": [],
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"source": [
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{
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"cell_type": "markdown",
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"source": [
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"the final result should be 10:"
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"outputs": [],
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"source": [
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{
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"cell_type": "markdown",
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"source": [
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"we can also check the results of two other nodes:"
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"outputs": [],
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"source": [
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎notebooks/basic_nodes.ipynb

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"outputs": [],
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"source": [
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"# Specify node inputs\n",
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"bet.inputs.in_file = '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz'\n",
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"bet.inputs.in_file = '/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz'\n",
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"bet.inputs.out_file = '/output/node_T1w_bet.nii.gz'"
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]
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},
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"\n",
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"# Define a node\n",
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"smooth_node = Node(IsotropicSmooth(), name=\"smoothing\")\n",
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"smooth_node.inputs.in_file = '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz'\n",
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"smooth_node.inputs.in_file = '/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz'\n",
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"smooth_node.inputs.fwhm = 4\n",
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"smooth_node.inputs.out_file = '/output/node_T1w_smooth.nii.gz'\n",
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"smooth_res = smooth_node.run()\n"
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

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