Replace JNIfTI by JNIFTI in makefile macros

in the BIDS (.json) sidecar in cose of image interpolation.

TotalReadoutTime and EffectiveEchoSpacing were correct when there was
no interpolation (i.e. AcquisitionMatrixPE = ReconMatrixPE).
However, when interpolation was used, this values were incorrect.
When interpolation was used, the estimated fieldmap given by TOPUP
was ReconMatrixPE/AcquisitionMatrixPE times a measured fieldmap.
Also, the same interpolated images corrected with a B0Map based method
via FSL's epi_reg were clearly under-corrected.
It turned out that the problem was comming from TotalReadoutTime and
EffectiveEchoSpacing which were not taking ReconMatrixPE correctly
into account.
This is a Fix for that.

GE/README.md was modified to clarified how TotalReadoutTime and
EffectiveEchoSpacing are now computed.
Some intermediate variable were also introduced and this described.
This should help he final user to better understand.

console/nii_dicom_batch.cpp was modified to implement the changes on
TotalReadoutTime and EffectiveEchoSpacing.
The intermediate variables described in README were also added into
the json BIDS sidecar (i.e. EchoSpacingMicroSecondsGE,
NotPhysicalNumberOfAcquiredPELinesGE, NotPhysicalTotalReadOutTimeGE).
As the TotalReadoutTime definition is not intuitive this should
help the user to understand what is going on.

On branch dev-fix-TotalReadoutTimeGE-with-interpolation
Changes to be committed:
	modified:   GE/README.md
	modified:   console/nii_dicom_batch.cpp

…interpolation

Dev fix TotalReadoutTime for GE with interpolation

  1. save dicom file list in MRIFSSTRUCT, return vector of MRIFSSTRUCT for multi-echo scans if isForceStackSameSeries = 0 (-m n)
  2. change output file format to "%4s.%d" from "%4s.%p" to be consistent with Freesurfer dcmunpack
  3. remove space, [, ] from scan description
  4. implement isDumpNotConvert option to retrieve dicom info only
  5. dcm2niix_fswrapper::dicomDump() - output information of series to be converted, and seriesNum-dicomflst.txt in the same directory as series-info.dat;
     dcm2niix_fswrapper::seriesInfoDump() - print information for given dicom series
  6. don't use std::max() from <algorithm> (fix Freesurfer ubuntu18 compiler error)

It is now clarified that the `EchoSpacing` variable is the GE private
DICOM field "(0043,102C) Effective Echo Spacing".

On branch fix-documentation-GE-TotalReadoutTime
Changes to be committed:
	modified:   GE/README.md

…tTime

Documentation fix for GE TotalReadoutTime.

Fix typos in GE/README.md and code mofification to add the intermediate variables
for TotalReadoutTime on GE system in debug mode only (via compilation flag MY_DEBUG).

Added a note for that in GE/README.md:

For debugging purposes, the intermediate variables `NotPhysicalTotalReadOutTimeGE`, `NotPhysicalNumberOfAcquiredPELinesGE` and `EchoSpacing` (renamed `EchoSpacingMicroSecondsGE`) are written to the BIDS-sidecar JSON file when dcm2niix is compiled with the flag `MY_DEBUG`.

On branch dev-fix-GETotalReadoutTime-doc-and-code
Changes to be committed:
	modified:   GE/README.md
	modified:   console/nii_dicom_batch.cpp

…nd-code

Fix code and doc for GE TotalReadoutTime

dcm2niix_fswrapper and libdcm2niixfs.a

3db0map

issue 769: Mildly relax the check for bvec components > 1.

fixes #773

Thanks!

Development

…nto development

Fix PhaseEncodingDirectionDisplayed for GE #779

…operation

…library

Changes from divest v1.0