5TTmsmt: inclusion of -sgm_amyg_hipp option#3401
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voxel2mesh fixes
Conflicts: lib/mrtrix3/fsl.py
- Previously, if -iter 1 was specified, the weights were not recomputed, and so results were identical to that with -iter 0. - Do not unnecessarily recompute weights at completion of the final iteration.
dwi2tensor: fix operation with -iter 1
…read_with_unsupported_transfer_syntax
…with_unsupported_transfer_syntax DICOM: add null imageIO handler to allow parsing of DICOM data even with unsupported transfer syntax
Tolerance for dw_scheme differences on header merge
…om_position DICOM: ignore image positioning tags if nested within Philips private sequence
For consistency and to avoid potential conflicts in external projects.
This addresses an issue raised on the forum, and is due to our use of a write-back buffer (to prevent file segmentation) with a default size of 16MB. This is ample for regular streamlines, but clearly not enough in all cases... Original issue: https://community.mrtrix.org/t/tckgen-seed-point-visualization/8271/2
Merge branch 'master' into 'dev'
…dling dwi2mask hdbet: Fix exception handling
- Fix progress bar for when FSL FAST is not used for the cerebellum, and the FreeSurfer segmentations of the cerebellar hemispheres are propagated to the 5TT image. - New option -freesurfer_lut, for manually specifying the location of the FreeSurfer lookup table file; this permits utilisation of the script without environment variable FREESURFER_HOME being set, or indeed even the FreeSurfer software being present (related to MRtrix3#3073). - Add missing citations to help page documentation.
5ttgen hsvs: Multiple changes / fixes
Erroneous omission from f99f80e.
…eamline Fix tck writer when a single streamline exceed the buffer size
FIX: don't build gui subdirectory with BUILD_GUI=OFF
Re-applies changes in MRtrix3#3056 that were lost on dev branch as a consequence of MRtrix3#3061.
Update clang-tidy-review action to v0.20.1
…pply dwi2tensor: Fix operation with -iter 1 (re-apply)
Conflicts: testing/CMakeLists.txt
5ttgen: Add Deep Atropos algorithm
Conflicts: testing/CMakeLists.txt
fod2fixel: New metric "skew"
Conflicts: cmd/dirflip.cpp cmd/dirgen.cpp cpp/cmd/dirorder.cpp
This keeps the command-line option name consistent with the similar functionality in the dirflip command.
Includes thos functionalities relating to the preservation of directions at the head of direction sets, but also adds tests for default functionality of dirflip and dirorder not yet present.
Conflicts: cpp/cmd/mrcalc.cpp cpp/cmd/peaksconvert.cpp cpp/core/file/nifti_utils.h
dir* command modifications for fixed direction handling
This reference frame appears to be an intrinsic feature of the FSL software and not specific to the encoding of diffusion MRI sensitisation directions in the .bvec format.
- All calculations observed throughout the code base that relate to relationships between cartesian and spherical coordinates, as well as spherical harmonics, make reference to the cosine of the second angle as its component relative to the zenith. This would make that angle an inclination rather than an elevation.
Conflicts: testing/CMakeLists.txt
Resolves original implementation created in MRtrix3#2918 against post-cmake Python changes.
Option facilitates nominating which references axis set the input dataset is expected a priori to conform to; the terminal feedback & command error code are modulated accordingly.
Partial reversion of 3ddf174.
New commands: peaksconvert, peakscheck
Port unit tests to Google Test
Remove command shbasis
Conflicts: docs/reference/commands/5ttgen.rst python/mrtrix3/commands/5ttgen/__init__.py testing/CMakeLists.txt
Default run (steps 1-4) uses ODF-derived tissue fractions directly with masking and CSF fill to guarantee sum=1. FSL FIRST (sub-cortical GM) and FAST (intensity-guided tissue refinement) now only execute when the user passes -sgm_amyg_hipp.
…e from masking. no harm in filling SGM structures, so leave as is. this commit uses different masking strategy (volsum > 0)
…l (invert → connect-largest → invert) → dilate ×3 → erode ×3
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This PR adds a new msmt algorithm to 5ttgen, which derives a 5TT image directly from multi-shell multi-tissue (MSMT) ODF images (odf_wm, odf_gm, odf_csf) rather than relying on a T1-weighted image.
Default pipeline (no FSL required):
ODF l=0 terms are extracted, normalised to sum to 1.0, and assembled into a 5TT image. A brain mask is generated from the ODF volume sum using a morphological pipeline (threshold → clean → connect-largest → dilate×3 → erode×3). A CSF-fill step ensures tissue fractions sum to exactly 1.0 in all brain voxels.
Optional sub-cortical GM segmentation via -sgm_amyg_hipp:
When this flag is passed, FSL FIRST is used to segment sub-cortical GM structures (including amygdala and hippocampus), and FSL FAST is used for intensity-guided tissue refinement. A vis image derived from the initial 5TT (via 5tt2vis) is used as a T1-surrogate for both tools. Availability of FSL tools is checked at runtime, with fallback and warnings if tools are missing.
Target branch: dev