pnlbwh/dMRIharmonization

Issues

• image of mean FA is not appropriate

  #90 opened 4 months ago by ShivyaGupta14
  9

• Denoising Step

  #88 opened 5 months ago by jenna1029
  1

• dipy v 1.1.1 not comaptible

  #91 opened 4 months ago by ShivyaGupta14
  0

• Version/Attribute Issue at Template Creation (n is not an attribute of QballModel)

  #89 opened 4 months ago by ShivyaGupta14
  6

• nibabel library: get_data() is deprecated, and we should start using get_fdata() instead.

  #87 opened 7 months ago by suheyla2
  0

• Different data for template creation and harmonization, how to find the goodness of harmonization by observing the number after harmonization

  #77 opened 9 months ago by jwchen03
  4

• Conflicting starting meanFA values for each site depending on the direction of the harmonization.

  #78 opened 9 months ago by pall75
  16

• Compressed file ended before the end-of-stream marker was reached

  #82 opened 9 months ago by LucaGherardini
  3

• Pipeline_test.sh values not matching expected

  #86 opened 9 months ago by jenna1029
  1

• IIT atlas file links in README need update or causing ANTS and ITK ImageReader error

  #85 opened 2 years ago by Lanyavikins
  0

• Segmentation fault in lantsMultivariateTemplateConstruction2_fixed_random_seed.sh

  #84 opened 2 years ago by yoshito656
  0

• Time estimate for template

  #83 opened 2 years ago by nancynewlin-masi
  1

• Path with dots breaks `antsMultivariateTemplateConstruction2.sh`

  #80 opened 3 years ago by njhunsak
  30

• N_shm=-1 is not overwritten in config

  #79 opened 3 years ago by tashrifbillah
  0

• Applying the harmonization to other diffusion weighted images

  #73 opened 4 years ago by JoaoPaulo100
  8

• Remove outdated comments

  #76 opened 4 years ago by tashrifbillah
  0

• Skipping unring step

  #74 opened 4 years ago by josephmje
  2

• [Redundancy] Do not redo registration for harmonized data

  #64 opened 4 years ago by tashrifbillah
  0

• tests run N_shm key error

  #65 opened 4 years ago by vsiless
  5

• Missing Scale_L4

  #68 opened 4 years ago by peterN908
  7

• b-values near 0 being remapped to `bNew`

  #71 opened 4 years ago by kcho
  2

• Harmonizing patients to healthy controls

  #70 opened 4 years ago by hughmt
  1

• processing data from reference site, which were not included in the template creation step

  #69 opened 4 years ago by kcho
  2

• Use mkstemp to generate a named temporary file

  #63 opened 5 years ago by tashrifbillah
  4

• [redundancy] compute masked volume inside DIPY block

  #62 opened 5 years ago by tashrifbillah
  1

• harmonization of 1.5T and 3T scanners

  #61 opened 5 years ago by tashrifbillah
  0

• Harmonization for pediatric/neonatal datasets

  #60 opened 5 years ago by mblesac
  1

• TODO: spherical harmonics model needs to be fitted on REF site w/o any scaling

  #48 opened 5 years ago by tashrifbillah
  4

• data harmonization in TBI patients

  #56 opened 5 years ago by fedemoro
  1

• Challenge the program with --resample --debug --force

  #58 opened 5 years ago by tashrifbillah
  1

• Replacing SPM, FSL, REISERT tools with standard Python packages

  #59 opened 5 years ago by tashrifbillah
  1

• Expected meanFAstats.txt from the pipeline_test.sh

  #45 opened 5 years ago by kcho
  4

• TODO: structure the output statistics file

  #47 opened 5 years ago by tashrifbillah
  6

• Preserve singularity of qform() and sform() individually

  #49 opened 5 years ago by tashrifbillah
  1

• setting smooth parameter for SH fitting to a smaller value

  #52 opened 5 years ago by suheyla2
  0

• Can --ref_name and --tar_name be not mandatory?

  #50 opened 5 years ago by tashrifbillah
  1

• Replace `aramislab` by pnlbwh`

  #53 opened 5 years ago by tashrifbillah
  1

• Data path parcellation

  #44 opened 5 years ago by suheyla2
  8

• os module is not imported in the `test_util.py` nor `fa_skeleton_test.py`

  #42 opened 5 years ago by kcho
  1

• path in a line 194 in README.md

  #41 opened 5 years ago by kcho
  2

• Optimize spm_bspline execution to avert memory error

  #37 opened 5 years ago by tashrifbillah
  1

• Provide --ncpu for multivariate template construction and the rest differently

  #38 opened 5 years ago by tashrifbillah
  1

• Resampled mask in Python is zero on the last slice along Z axis

  #29 opened 5 years ago by tashrifbillah
  8

• Resume stopped template creation

  #34 opened 5 years ago by fedemoro
  7

• Use soft thresholding to identify b0

  #32 opened 5 years ago by tashrifbillah
  2

• tmp dir

  #31 opened 5 years ago by fedemoro
  9

• pipeline_test.sh

  #26 opened 5 years ago by fedemoro
  3

• print all FA statistics, mean FA, std FA

  #27 opened 5 years ago by tashrifbillah
  2

• Add imagelist generation instruction in README.md

  #24 opened 5 years ago by tashrifbillah
  2

• MATLAB Runtime Compiler

  #25 opened 5 years ago by fedemoro
  1