Remove external dependencies

[tashrifbillah]

Follow up from work group on 1/29/2020:

A few external dependencies can be removed readily:

https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/blob/master/pipeline/pipeline_requirements.txt

(i) nrrd library - To check nhdr/nrrd Image header

• [x] unu is no longer required given our development with pynrrd

(ii) ResampleImage - To Resample the input Image

• [x] @SenthilCaesar noted this is unused

(iii)

bse.sh - To extract b0 from nhdr/nrrd Image
dwiextract - To extract b0 from nifti Image

• [x] DWI should first be converted to nifti using nifti_write.py and then bse should be extracted using pnlNipype/scripts/bse.py

(iv) ConvertBetweenFileFormats - To Convert ndhr/nrrd to nifti files

• [x] Once the above are satisfied, this becomes irrelevant.

(v) FSL FLIRT - To perform Image Registration

• [x] @SenthilCaesar noted ANTs is being used now.

cc: @yrathi @suheyla2 @sbouix

[tashrifbillah]

If we following the steps:

        # convert NRRD/NHDR to NIFIT as the first step
        # extract bse.py from just NIFTI later

then, (i) and (iv) are out of the picture.

[tashrifbillah]

(iii) nifti_write.py has been applied

Fixed by https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/commit/c18b5f5bc51b955a07e55b52e35f9b5ea0528a0f

[tashrifbillah]

• [x] maskfilter from mrtrix

[tashrifbillah]

• maskfilter from mrtrix commented out
• Python translated maskfilter added https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/commit/b3deb00c27cb55727394e69e9e53b6cdfdd0a292

[tashrifbillah]

• [x] @tashrifbillah and @SenthilCaesar will test the Python translated maskfilter on 10 b0 images.

[tashrifbillah]

• [ ] remove slicesdir from FSL FUTURE

[tashrifbillah]

Senthil's experiment of python translated src/maskfilter:

[tashrifbillah]

Kept option for mrtrix and src/maskfilter