Release Name: 0.3.5
Notes:
0.3.5
ASL and PD support, Mac build, incremental improvements
* Feature: Support for ASL (perfusion) images. Intended for Siemens
PCASL and Philips PASL. Not needed for older PASL and GE PCASL
sequences.
* Feature: Support for PD-weighted images. This uses the same
template and settings as T2-w images. Dual-echo T2/PD, PD/T2 are
also supported. Thanks Cally Xiao for testing.
* Enhancement: MEGRE MRI: Allow face intensity and noise matching
to vary across volumes/echoes.
* Feature: New "coregistered4D" option: Allows overriding default
assumptions about which image types are coregistered and which are
not, e.g. if multi-echo MRI are acquired over time, or PET frames
were pre-aligned during preprocessing
* Feature: New options "TIVTolerance" and "TIVToleranceOffset" to
adjust the boundary between brain and face if necessary (e.g. if
outputs changed a few voxels of brain, but were otherwise good,
this may help).
* Feature: New Mac build (non-Docker only; Matlab does not support
building Docker images for non-Linux). This has the same
requirements as current Linux builds: Matlab2022a runtime (free),
reg_aladin (niftyreg), ANTS. Tested on MacOS Sequoia 15.1.1 with an
M2 "Silicon" chip. DICOM support was tested with dcm2niix (20241208
from Macports) and Python (3.10.16 from Macports) with modules
pydicom 3.0.1 and nibabel 5.3.2.
* Fix: Use a new and smaller mask for sampling air, preventing
errors in scans with extra-large heads and lots of motion.
* Docker: Optimized the Docker image to 5.4G unzipped / 2.3G
zipped. 0.3.3 was 7.5G / 5G respectively.
* ADIR_nii2dicom: ignore .txt and rawdata (non-image/exam card)
DICOM in DICOM folders
* ADIR_nii2dicom: improved handling for DICOM where some tags are
inconsistently present/absent. They will be considered inconsistent
and will not be copied.
* ADIR_nii2dicom: Add support for dropping frames from output
DICOM, or ignoring DICOM from frames already dropped from the input
nii
* ADIR_nii2dicom: Handling for DICOM with StackID and
DimensionIndexSequence/Values (were needed for ASL)
0.3.4 (not publicly released)
Additional PET image types support, improved PET noise models, and
minor enhancements
* Enhancement: Improved noise-matching models in the replacement
face for PET input types. Old noise added to NF PET, especially in
air, were too much. This now better matches input images.
* Feature: Added support for "early" and full-dynamic PET (treated
the same as each other). These activate automatically when given
PET inputs with >=10 frames
* For these, the last frame is used as the reference,
instead of the first, and frames at the start of the sequence with
significantly less signal than those in the middle of the sequence
are skipped from de-facing (copied as-is). These tweaks adjust for
the presence of frames in the first few minutes that typically lack
enough signal to warrant de-facing or to use as an anatomic
refrence
* Feature: Added support for PET tracers: PI2620 (treated like FTP)
and NAV4694 (treated like PIB)
* Feature: Added support for BIDS image type names (e.g. "T1w") in
automatic image-type guessing
* Fix: Prevent some crashes when input frames are empty (all
zeros)
* ADIR_nii2dicom: minor enhancements and fixes
Changes:
0.3.5
ASL and PD support, Mac build, incremental improvements
* Feature: Support for ASL (perfusion) images. Intended for Siemens
PCASL and Philips PASL. Not needed for older PASL and GE PCASL
sequences.
* Feature: Support for PD-weighted images. This uses the same
template and settings as T2-w images. Dual-echo T2/PD, PD/T2 are
also supported. Thanks Cally Xiao for testing.
* Enhancement: MEGRE MRI: Allow face intensity and noise matching
to vary across volumes/echoes.
* Feature: New "coregistered4D" option: Allows overriding default
assumptions about which image types are coregistered and which are
not, e.g. if multi-echo MRI are acquired over time, or PET frames
were pre-aligned during preprocessing
* Feature: New options "TIVTolerance" and "TIVToleranceOffset" to
adjust the boundary between brain and face if necessary (e.g. if
outputs changed a few voxels of brain, but were otherwise good,
this may help).
* Feature: New Mac build (non-Docker only; Matlab does not support
building Docker images for non-Linux). This has the same
requirements as current Linux builds: Matlab2022a runtime (free),
reg_aladin (niftyreg), ANTS. Tested on MacOS Sequoia 15.1.1 with an
M2 "Silicon" chip. DICOM support was tested with dcm2niix (20241208
from Macports) and Python (3.10.16 from Macports) with modules
pydicom 3.0.1 and nibabel 5.3.2.
* Fix: Use a new and smaller mask for sampling air, preventing
errors in scans with extra-large heads and lots of motion.
* Docker: Optimized the Docker image to 5.4G unzipped / 2.3G
zipped. 0.3.3 was 7.5G / 5G respectively.
* ADIR_nii2dicom: ignore .txt and rawdata (non-image/exam card)
DICOM in DICOM folders
* ADIR_nii2dicom: improved handling for DICOM where some tags are
inconsistently present/absent. They will be considered inconsistent
and will not be copied.
* ADIR_nii2dicom: Add support for dropping frames from output
DICOM, or ignoring DICOM from frames already dropped from the input
nii
* ADIR_nii2dicom: Handling for DICOM with StackID and
DimensionIndexSequence/Values (were needed for ASL)
0.3.4 (not publicly released)
Additional PET image types support, improved PET noise models, and
minor enhancements
* Enhancement: Improved noise-matching models in the replacement
face for PET input types. Old noise added to NF PET, especially in
air, were too much. This now better matches input images.
* Feature: Added support for "early" and full-dynamic PET (treated
the same as each other). These activate automatically when given
PET inputs with >=10 frames
* For these, the last frame is used as the reference,
instead of the first, and frames at the start of the sequence with
significantly less signal than those in the middle of the sequence
are skipped from de-facing (copied as-is). These tweaks adjust for
the presence of frames in the first few minutes that typically lack
enough signal to warrant de-facing or to use as an anatomic
refrence
* Feature: Added support for PET tracers: PI2620 (treated like FTP)
and NAV4694 (treated like PIB)
* Feature: Added support for BIDS image type names (e.g. "T1w") in
automatic image-type guessing
* Fix: Prevent some crashes when input frames are empty (all
zeros)
* ADIR_nii2dicom: minor enhancements and fixes
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