> 下面是被转发的邮件:
> 
> 发件人: YC Yao <yao_yongch...@icloud.com>
> 主题: 回复: [HCP-Users] how to map cortical thickness data to 180 parcellation 
> (Glasser et al, Nature)
> 日期: 2016年10月18日 GMT+8 18:57:22
> 收件人: Timothy Coalson <tsc...@mst.edu>, mha...@wustl.edu
> 
> Dear Tim and Michael Harms,
> 
> Thank your for your reply!
> I have already mapped the Freesurfer native individual data to fs_LR as 
> described in 
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersF 
> <https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersF>AQ-9.HowdoImapdatabetweenFreeSurferandHCP?
> 
> As suggested, I am supposed to use -cifti-create-dense-from-template to make 
> the cifti file containing thickness data, and then use -cifti-parcellate. But 
> I don’t know which subcommand and file to use after checking the 
> corresponding info:
> 
> CREATE CIFTI WITH MATCHING DENSE MAP
>    wb_command -cifti-create-dense-from-template
>       <template-cifti> - file to match brainordinates of
>       <cifti-out> - output - the output cifti file
> 
>       [-series] - make a dtseries file instead of a dscalar
>          <step> - increment between series points
>          <start> - start value of the series
> 
>          [-unit] - select unit for series (default SECOND)
>             <unit> - unit identifier
> 
>       [-volume-all] - specify an input volume file for all voxel data
>          <volume-in> - the input volume file
> 
>          [-from-cropped] - the input is cropped to the size of the voxel data
>             in the template file
> 
>       [-cifti] - repeatable - use input data from a cifti file
>          <cifti-in> - cifti file containing input data
> 
>       [-metric] - repeatable - use input data from a metric file
>          <structure> - which structure to put the metric file into
>          <metric-in> - input metric file
> 
>       [-label] - repeatable - use input data from surface label files
>          <structure> - which structure to put the label file into
>          <label-in> - input label file
> 
>       [-volume] - repeatable - use a volume file for a single volume
>          structure's data
>          <structure> - which structure to put the volume file into
>          <volume-in> - the input volume file
> 
>          [-from-cropped] - the input is cropped to the size of the volume
>             structure
> 
>       This command helps you make a new dscalar, dtseries, or dlabel cifti 
> file
>       that matches the brainordinate space used in another cifti file.  The
>       template file must have the desired brainordinate space in the mapping
>       along the column direction (for dtseries, dscalar, dlabel, and symmetric
>       dconn this is always the case).  All input cifti files must have a brain
>       models mapping along column and use the same volume space and/or surface
>       vertex count as the template for structures that they contain.  If any
>       input files contain label data, then input files with non-label data are
>       not allowed, and the -series option may not be used.
> 
>       Any structure that isn't covered by an input is filled with zeros or the
>       unlabeled key.
> 
>       The <structure> argument of -metric, -label or -volume must be one of 
> the
>       following:
> 
>       CORTEX_LEFT
>       CORTEX_RIGHT
>       CEREBELLUM
>       ACCUMBENS_LEFT
>       ACCUMBENS_RIGHT
>       ALL_GREY_MATTER
>       ALL_WHITE_MATTER
>       AMYGDALA_LEFT
>       AMYGDALA_RIGHT
>       BRAIN_STEM
>       CAUDATE_LEFT
>       CAUDATE_RIGHT
>       CEREBELLAR_WHITE_MATTER_LEFT
>       CEREBELLAR_WHITE_MATTER_RIGHT
>       CEREBELLUM_LEFT
>       CEREBELLUM_RIGHT
>       CEREBRAL_WHITE_MATTER_LEFT
>       CEREBRAL_WHITE_MATTER_RIGHT
>       CORTEX
>       DIENCEPHALON_VENTRAL_LEFT
>       DIENCEPHALON_VENTRAL_RIGHT
>       HIPPOCAMPUS_LEFT
>       HIPPOCAMPUS_RIGHT
>       INVALID
>       OTHER
>       OTHER_GREY_MATTER
>       OTHER_WHITE_MATTER
>       PALLIDUM_LEFT
>       PALLIDUM_RIGHT
>       PUTAMEN_LEFT
>       PUTAMEN_RIGHT
>       THALAMUS_LEFT
>       THALAMUS_RIGHT
> 
>       The argument to -unit must be one of the following:
> 
>       SECOND
>       HERTZ
>       METER
>       RADIAN
> 
> 
> PARCELLATE A CIFTI FILE
>    wb_command -cifti-parcellate
>       <cifti-in> - the cifti file to parcellate
>       <cifti-label> - a cifti label file to use for the parcellation
>       <direction> - which mapping to parcellate (integer, ROW, or COLUMN)
>       <cifti-out> - output - output cifti file
> 
>       [-spatial-weights] - use voxel volume and either vertex areas or metric
>          files as weights
> 
>          [-left-area-surf] - use a surface for left vertex areas
>             <left-surf> - the left surface to use, areas are in mm^2
> 
>          [-right-area-surf] - use a surface for right vertex areas
>             <right-surf> - the right surface to use, areas are in mm^2
> 
>          [-cerebellum-area-surf] - use a surface for cerebellum vertex areas
>             <cerebellum-surf> - the cerebellum surface to use, areas are in
>                mm^2
> 
>          [-left-area-metric] - use a metric file for left vertex weights
>             <left-metric> - metric file containing left vertex weights
> 
>          [-right-area-metric] - use a metric file for right vertex weights
>             <right-metric> - metric file containing right vertex weights
> 
>          [-cerebellum-area-metric] - use a metric file for cerebellum vertex
>             weights
>             <cerebellum-metric> - metric file containing cerebellum vertex
>                weights
> 
>       [-cifti-weights] - use a cifti file containing weights
>          <weight-cifti> - the weights to use, as a cifti file
> 
>       [-method] - specify method of parcellation (default MEAN, or MODE if
>          label data)
>          <method> - the method to use to assign parcel values from the values
>             of member brainordinates
> 
>       [-exclude-outliers] - exclude non-numeric values and outliers from each
>          parcel by standard deviation
>          <sigma-below> - number of standard deviations below the mean to
>             include
>          <sigma-above> - number of standard deviations above the mean to
>             include
> 
>       [-only-numeric] - exclude non-numeric values
> 
>       Each label in the cifti label file will be treated as a parcel, and all
>       rows or columns within the parcel are averaged together to form the
>       output row or column.  The direction can be either an integer starting
>       from 1, or the strings 'ROW' or 'COLUMN'.  For dtseries or dscalar, use
>       COLUMN.  If you are parcellating a dconn in both directions, 
> parcellating
>       by ROW first will use much less memory.
> 
>       The parameter to the -method option must be one of the following:
> 
>       MAX: the maximum value
>       MIN: the minimum value
>       INDEXMAX: the 1-based index of the maximum value
>       INDEXMIN: the 1-based index of the minimum value
>       SUM: add all values
>       PRODUCT: multiply all values
>       MEAN: the mean of the data
>       STDEV: the standard deviation (N denominator)
>       SAMPSTDEV: the sample standard deviation (N-1 denominator)
>       VARIANCE: the variance of the data
>       TSNR: mean divided by sample standard deviation (N-1 denominator)
>       COV: sample standard deviation (N-1 denominator) divided by mean
>       MEDIAN: the median of the data
>       MODE: the mode of the data
>       COUNT_NONZERO: the number of nonzero elements in the data
> 
>       The -*-weights options are mutually exclusive and may only be used with
>       MEAN, SUM, STDEV, SAMPSTDEV, VARIANCE, MEDIAN, or MODE.
> 
> To recap:
> My aim is to map the freesurfer lh.thickness and rh.thickness data to 180 
> parcellation (Glasser et al).
> 
> New files created: 
> (subject name:FeSZ_08_0004)
> 1. (after running: mris_convert -c lh.thickness lh.white lh.thickness.gii)
> surf/lh.thickness.gii
> 
> 2.(after running wb_shortcuts -freesurfer-resample-prep )
> surf/FeSZ_08_0004.lh.midthickness.32k_fs_LR.surf.gii
> surf/lh.midthickness.surf.gii
> surf/lh.sphere.reg.surf.gii
> 
> 3.(after running  "wb_command -metric-resample” )
> surf/FeSZ_08_0004.ADAP_BARY_AREA.lh.32k_fs_LR.func.gii 
> 
> Do I need to use files from /standard_mesh_atlases ?
> Would you explicitly explain which subcommand should I use and which file 
> should I use?
> 
> Best,
> YC Yao
> 
> 


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