The options to these commands aren't subcommands, they just provide input data or modify the details of how the command works.
For -cifti-create-dense-from-template, you can use the dlabel file as the template (since you only plan to parcellate the data, it isn't critical to match them to the 91282 grayordinate space), then specify -metric twice, for left and right thickness files. For -cifti-parcellate, use the file you just created with -cifti-create-dense-from-template, use COLUMN for the direction, and it would be good to use -spatial-weights and the group average vertex area metrics (these happen to exist in the resampling files, fs_LR.L.midthickness_va_avg.32k_fs_LR.shape.gii and fs_LR.R.midthickness_va_avg.32k_fs_LR.shape.gii). If you run into trouble with them, you can do it without -spatial-weights and get a similar answer. Tim On Tue, Oct 18, 2016 at 5:59 AM, YC Yao <yao_yongch...@icloud.com> wrote: > > > 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 > 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 > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
