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= mri_overlap = = mri_seg_overlap =
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This page proposes a new program, called `mri_overlap`, that will replace the redundant (and buggy/slow) `mri_compute_seg_overlap` and `mri_compute_overlap`. A primary new feature is the ability to save a detailed overlap report to a JSON file. This page proposes a new program, called `mri_seg_overlap`, that will replace the redundant (and buggy/slow) `mri_compute_seg_overlap` and `mri_compute_overlap`. A primary new feature is the ability to save a detailed overlap report to a JSON file.
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USAGE: USAGE
 mri_seg_overlap [options] <vol1> <vol2>
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    mri_overlap <vol1> <vol2> [options] DESCRIPTION
 
 This program computes the structural overlap between two segmentation
 volumes. The following statistics can be calculated for each label:
 
      dice coefficient - F1-measure of the similarity between
                              the two labels.
      jaccard coefficient - Intersecting volume over the combined
                              volume of the two labels.
      volume difference - Fractional difference in volumes of
                              the labels.
 
 By default, only dice scores are computed, but this can be
 reconfigured with the --measures flag.
 
 Each structure in the input volumes will be considered by default, but
 an alternative list of labels can be specified with the --label or --labelfile
 flags. Additionally, the --seg flag will compute the overlap between
 the following 12 major anatomical structures:
 
      Cerebral White Matter (2,41)
      Cerebral Cortex (3,42)
      Hippocampus (17,53)
      Caudate (11,50)
      Putamen (12,51)
      Pallidum (13,52)
      Amygdala (18,54)
      Thalamus Proper (10,49)
      Lateral Ventricle (4,43)
      Third and Fourth Ventricles (14,15)
      Inf Lateral Vent (5,44)
      Accumbens Area (26,58)
  
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DESCRIPTION: OPTIONAL ARGUMENTS
 -o, --out [FILE]
  Save detailed overlap report to a JSON file.
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    This program computes the overlap between two segmentation volumes. The following
    statistics can be calculated for each label:		  -m, --measures [MEASURE...]
  List of measures to compute. By default, only dice scores are
  computed. Options include: dice, jaccard, voldiff
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        dice coefficient - F1-measure of the similarity between the two labels
        jaccard coefficient - intersecting volume over the combined volume of the two labels
        volume difference - fractional difference between the label volumes		  -l, --labels [LABEL...]
  Space-separated list of label values to include. By default,
  the overlap will be computed between all labels available in
  both input volumes.
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    By default, only dice scores are computed, but this can be reconfigured
    with the --measures flag.		  -n, --names [LABELNAME...]
  Custom label names corresponding to the values specified with
  the --labels flag.
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    Each structure in the input volumes will be considered by default, but
    an alternative list of labels can be specified with the -l flag. Additionally,
    the --seg flag will compute the overlap between the following 12 major
    anatomical structures:		  -f, --labelfile [FILE]
  Text file specifying the label values to include. This file
  must be in the format of a freesurfer lookup-table, in which
  each line contains a label value and, optionally, a
  corresponding label name.
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        Hippocampus (17,53)
        Caudate (11,50)
        Putamen (12,51)
        Pallidum (13,52)
        Amygdala (18,54)
        Thalamus Proper (10,49)
        Lateral Ventricle (4,43)
        Third and Fourth Ventricles (14,15)
        Inf Lateral Vent (5,44)
        Cerebral White Matter (2,41)
        Cerebral Cortex (3,42)
        Accumbens Area (26,58)		  -x, --no-names
  Do not report label names.
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OPTIONAL ARGUMENTS:  -s, --seg
  Compute overlap between the the major segmentation structures
  listed above.
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    -o, --out
        Save detailed overlap report to a JSON file.		  -q, --quiet
  Quiet mode - do not print results to stdout.
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    -m, --measures
        List of measures to compute. By default, only dice scores
        are computed. Options include: dice, jaccard, voldiff

    -l, --labels
        Space-separated list of label values to include. By default, the overlap
        will be computed between all labels available in both input volumes.

    -f, --labelfile
        File specifying a list of labels to include. This file can either be a
        space-separated list of label values or in the format of a freesurfer
        color lookup-table.

    -s, --seg
        Compute overlap between the major segmentation structures listed above.
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The proposed JSON output would look something like this: NOTE: if the `--seg` flag is used, an additional statistic called `weighted-subcortical-mean`, which ignores wm and cortex, will be reported for each measure.
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    "names": {
        "1": "structure 1",
        "2": "structure 2"
        ...
    },
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        "/path/to/manual_label.mgz",
        "/other/path/to/aseg.mgz"		         "/path/to/aseg.mgz",
        "/path/to/mseg.mgz"
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            "mean": 0.9142,
            "std": 0.0232,
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                "2": 0.9143,
                "3": 0.8739,
                "4": 0.9002,		                 "10": 0.9075892566820576,
                "11": 0.8953675962203272,
                "12": 0.9146751935375295,
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            }             },
            "mean": 0.6805390452588164,
            "std": 0.3237900375396044,
            "weighted-mean": 0.9340674985029207
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            "mean": 0.8902,
            "std": 0.0144,
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                "2": 0.8921,                 "10": 0.8308131920466723,
                "11": 0.8105570623826414,
                "12": 0.8427663203597457,
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            }
        },
        "voldiff": {
            "mean": 0.0221,
            "std": 0.0032,
            "labels": {
                "2": 0.0123,
                ...
            }		             },
            "mean": 0.5892475078628221,
            "std": 0.3029904264784899,
            "weighted-mean": 0.8801749135061013
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    },
    "names": {
        "10": "Left-Thalamus",
        "11": "Left-Caudate",
        "12": "Left-Putamen",
        ...

mri_seg_overlap

This page proposes a new program, called mri_seg_overlap, that will replace the redundant (and buggy/slow) mri_compute_seg_overlap and mri_compute_overlap. A primary new feature is the ability to save a detailed overlap report to a JSON file. 

USAGE
        mri_seg_overlap [options] <vol1> <vol2>

DESCRIPTION
        
        This program computes the structural overlap between two segmentation 
        volumes. The following statistics can be calculated for each label:
        
             dice coefficient     -  F1-measure of the similarity between
                                     the two labels.
             jaccard coefficient  -  Intersecting volume over the combined
                                     volume of the two labels.
             volume difference    -  Fractional difference in volumes of
                                     the labels.
        
        By default, only dice scores are computed, but this can be 
        reconfigured with the --measures flag.
        
        Each structure in the input volumes will be considered by default, but
        an alternative list of labels can be specified with the --label or --labelfile
        flags. Additionally, the --seg flag will compute the overlap between 
        the following 12 major anatomical structures:
        
             Cerebral White Matter (2,41)
             Cerebral Cortex (3,42)
             Hippocampus (17,53)
             Caudate (11,50)
             Putamen (12,51)
             Pallidum (13,52)
             Amygdala (18,54)
             Thalamus Proper (10,49)
             Lateral Ventricle (4,43)
             Third and Fourth Ventricles (14,15)
             Inf Lateral Vent (5,44)
             Accumbens Area (26,58)
         

OPTIONAL ARGUMENTS
        -o, --out [FILE]
                Save detailed overlap report to a JSON file.

        -m, --measures  [MEASURE...]
                List of measures to compute. By default, only dice scores are 
                computed. Options include: dice, jaccard, voldiff

        -l, --labels  [LABEL...]
                Space-separated list of label values to include. By default, 
                the overlap will be computed between all labels available in 
                both input volumes.

        -n, --names  [LABELNAME...]
                Custom label names corresponding to the values specified with 
                the --labels flag.

        -f, --labelfile  [FILE]
                Text file specifying the label values to include. This file 
                must be in the format of a freesurfer lookup-table, in which 
                each line contains a label value and, optionally, a 
                corresponding label name.

        -x, --no-names
                Do not report label names.

        -s, --seg
                Compute overlap between the the major segmentation structures 
                listed above.

        -q, --quiet
                Quiet mode - do not print results to stdout.

JSON

NOTE: if the --seg flag is used, an additional statistic called weighted-subcortical-mean, which ignores wm and cortex, will be reported for each measure. 

{
    "inputs": [
        "/path/to/aseg.mgz",
        "/path/to/mseg.mgz"
    ],
    "measures": {
        "dice": {
            "labels": {
                "10": 0.9075892566820576,
                "11": 0.8953675962203272,
                "12": 0.9146751935375295,
                ...
            },
            "mean": 0.6805390452588164,
            "std": 0.3237900375396044,
            "weighted-mean": 0.9340674985029207
        },
        "jaccard": {
            "labels": {
                "10": 0.8308131920466723,
                "11": 0.8105570623826414,
                "12": 0.8427663203597457,
                ...
            },
            "mean": 0.5892475078628221,
            "std": 0.3029904264784899,
            "weighted-mean": 0.8801749135061013
        }
    },
    "names": {
        "10": "Left-Thalamus",
        "11": "Left-Caudate",
        "12": "Left-Putamen",
        ...
    }
}

mri_overlap (last edited 2018-09-24 11:22:21 by AndrewHoopes)