prepare binder and basic jupyter notebook

[Remi-Gau]

Can be tried here: https://mybinder.org/v2/gh/Remi-Gau/CPP_BIDS_SPM_pipeline/remi-binder_notebook

There is a basic demo jupyter notebook in the notebooks folder.

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issues

• graphic output of the pipeline is not created (is it because this is like a command line mode?)
  • CmdLine = spm('CmdLine', false) --> returns 1 on binder. We won't be able to draw things.
• no output on the "prompt"
• create a separate jupyter book using python for interactive visualization of the results
• update README to explain how to run the notebook locally
• save options does not show where the file is save
• bidsResliceTpmToFunc does not run: WHY?

[Remi-Gau]

But at the moment I am getting some weird errors on the normalization in the spatial preprocessing.

In file "/home/jovyan/spm12/spm_deformations.m" (v6577), function "spm_deformations" at line 17.
In file "/home/jovyan/spm12/config/spm_run_norm.m" (v7406), function "spm_run_norm>write_norm" at line 111.
In file "/home/jovyan/spm12/config/spm_run_norm.m" (v7406), function "spm_run_norm" at line 29.

01-Nov-2020 08:21:28 - Running 'Normalise: Write'
01-Nov-2020 08:21:28 - Failed  'Normalise: Write'
file2mat.c not compiled - see Makefile
In file "/home/jovyan/spm12/@file_array/private/file2mat.m" (v7147), function "file2mat" at line 16.
In file "/home/jovyan/spm12/@file_array/subsref.m" (v7439), function "subsref>multifile2mat" at line 179.
In file "/home/jovyan/spm12/@file_array/subsref.m" (v7439), function "subsref>subfun" at line 99.
In file "/home/jovyan/spm12/@file_array/subsref.m" (v7439), function "subsref" at line 65.
In file "/home/jovyan/spm12/@nifti/subsref.m" (v7147), function "subsref>rec" at line 221.
In file "/home/jovyan/spm12/@nifti/subsref.m" (v7147), function "subsref" at line 45.
In file "/home/jovyan/spm12/spm_deformations.m" (v6577), function "spm_deformations>get_def" at line 192.
In file "/home/jovyan/spm12/spm_deformations.m" (v6577), function "spm_deformations>get_job" at line 78.
In file "/home/jovyan/spm12/spm_deformations.m" (v6577), function "spm_deformations>get_comp" at line 48.
In file "/home/jovyan/spm12/spm_deformations.m" (v6577), function "spm_deformations" at line 17.
In file "/home/jovyan/spm12/config/spm_run_norm.m" (v7406), function "spm_run_norm>write_norm" at line 111.
In file "/home/jovyan/spm12/config/spm_run_norm.m" (v7406), function "spm_run_norm" at line 29.

The following modules did not run:
Failed: Normalise: Write
Failed: Normalise: Write
Failed: Normalise: Write
Failed: Normalise: Write
Failed: Normalise: Write

error: Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
------------------ 
Running job #1
------------------

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Solution exists:

• "mat2file.c not compiled" when running SPM12 realign and reslice in an Octave-kernel Jupyter notebook spm/spm-notebooks#1
• https://jsheunis.github.io/2020-04-14-spm12-octave-binder/

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And it works 🎉

[codecov]

Codecov Report

Merging #155 (b47d046) into fmriprep_input (e6d2102) will increase coverage by 8.41%.
The diff coverage is 69.39%.

❗ Current head b47d046 differs from pull request most recent head 42bd261. Consider uploading reports for the commit 42bd261 to get more accurate results

@@                Coverage Diff                 @@
##           fmriprep_input     #155      +/-   ##
==================================================
+ Coverage           60.50%   68.92%   +8.41%     
==================================================
  Files                 125      133       +8     
  Lines                2056     2597     +541     
==================================================
+ Hits                 1244     1790     +546     
+ Misses                812      807       -5     

Impacted Files	Coverage Δ
src/QA/anatomicalQA.m	0.00% <0.00%> (ø)
src/QA/anatomicalQALesion.m	0.00% <0.00%> (ø)
src/QA/functionalQA.m	0.00% <0.00%> (ø)
src/batches/setBatchCoregistrationFuncToAnat.m	100.00% <ø> (ø)
src/batches/setBatchLesionAbnormalitiesDetection.m	0.00% <0.00%> (ø)
src/batches/setBatchLesionSegmentation.m	0.00% <0.00%> (ø)
src/batches/setBatchSelectAnat.m	100.00% <ø> (ø)
src/defaults/spm_my_defaults.m	100.00% <ø> (ø)
src/fieldmaps/getTotalReadoutTime.m	75.00% <0.00%> (+75.00%)	⬆️
src/templates/bidsTemplateWorkflow.m	0.00% <0.00%> (ø)
... and 120 more

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