Yaroslav Halchenko

dire need: BIDSFile helper

1

To be used in https://github.com/nipy/heudiconv/pull/441/files#diff-a48009f9efe6cc64ffdb74d06e831296R370 and in code introduced in #424 (number of locations like https://github.com/nipy/heudiconv/pull/424/files#diff-a48009f9efe6cc64ffdb74d06e831296R284). We need some lightweight (not yet full pybids) parsing of BIDS filenames, so we...

a command to list DICOM attributes of interest in a pile of DICOMs

1

attn @loj quite often it might be very handy to get a quick idea about some metadata within the pile of DICOMs. E.g. for establishing a heuristic or mapping into...

GE scanner pepolar maps - both AP and PA are in the same series/.nii.gz

14

I am helping to convert some data from GE DISCOVERY MR750 using heudiconv and EPI pepolar maps come as - Series Description `SE_EPI_B0`, PulseSequenceName `muxepi2` -- 8 dynamics (not yet...

Create/populate .bidsignore with .git (if datalad mode?) and .heudiconv

6

It seems that many BIDS tools might look outside of the standardized by BIDS locations, and thus end up in .git or in .heudiconv and then complain about their hard...

Dockerfile in this repo nicely and reproducibly installing elderly v1.0.20190410 ``` $> docker run -it --rm --entrypoint dcm2niix nipy/heudiconv:0.9.0 Chris Rorden's dcm2niiX version v1.0.20190410 GCC6.3.0 (64-bit Linux) ``` To add...

ENH: Use fscacher

1

We started to develop https://github.com/con/fscacher/ which could come handy for heudiconv, in particular for functions extracting desired metadata from dicom files. It would be great to avoid long wait times...

when tested as installed by `python3 -m pytest -s -v --pyargs heudiconv` it would fail since installed modules are not executable. We should either copy that file to temporary location...

subj/session is pretty much orthogonal, so we could at least place it under subj/session so later on bids-validator would alert us if it finds such non-standard files laying around.

More precise (to the month) age calculations are possible

1

ATM we are just taking PatientAge field, which is (typically) floored to the full years. NDA requires age in months, bids2nda rounds to the months according to the full years...

E.g. some of the tests working on axasc35.dcm would generate `Research/MCBI_TESTING/` ``` $> git grep -1 -p axasc heudiconv/tests/test_dicoms.py=def test_private_csa_header(tmpdir): heudiconv/tests/test_dicoms.py: dcm_file = op.join(TESTS_DATA_PATH, 'axasc35.dcm') heudiconv/tests/test_dicoms.py- dcm_data = dcm.read_file(dcm_file) --...