That command is meant for that purpose, yes, but you will first need to use one of the -cifti-create-* commands to make a template cifti in the downsampled space (you can use things like -surface-vertex-areas, -volume-create, and -volume-affine-resample to get the needed inputs for a -cifti-create-* command). I would also suggest considering parcellation instead of downsampling, so that the entirety of an area contributes to a single output value. Choosing a good parcellation for this is important, though.
Tim On Thu, Oct 29, 2015 at 2:36 PM, Jennifer Elam <[email protected]> wrote: > Hi, > > Tim C. can confirm, but if you are trying to resample a CIFTI fMRI data > file, such as a dense connectivity *.dconn, I would try using Connectome > Workbench <http://humanconnectome.org/software/connectome-workbench.html>: > wb_command -cifti-resample > > Here’s the help information > <http://humanconnectome.org/software/workbench-command.php> for the > -cifti-resample command: > > > > RESAMPLE A CIFTI FILE TO A NEW CIFTI SPACE > > wb_command -cifti-resample > > <cifti-in> - the cifti file to resample > > <direction> - the direction of the input that should be resampled > > <cifti-template> - a cifti file containing the cifti space to > resample to > > <template-direction> - the direction of the template to use as the > > resampling space > > <surface-method> - specify a surface resampling method > > <volume-method> - specify a volume interpolation method > > <cifti-out> - output - the output cifti file > > > > [-surface-largest] - use largest weight instead of weighted average > when > > doing surface resampling > > > > [-volume-predilate] - dilate the volume components before resampling > > <dilate-mm> - distance, in mm, to dilate > > > > [-surface-postdilate] - dilate the surface components after > resampling > > <dilate-mm> - distance, in mm, to dilate > > > > [-affine] - use an affine transformation on the volume components > > <affine-file> - the affine file to use > > > > [-flirt] - MUST be used if affine is a flirt affine > > <source-volume> - the source volume used when generating the > affine > > <target-volume> - the target volume used when generating the > affine > > > > [-warpfield] - use a warpfield on the volume components > > <warpfield> - the warpfield to use > > > > [-fnirt] - MUST be used if using a fnirt warpfield > > <source-volume> - the source volume used when generating the > > warpfield > > > > [-left-spheres] - specify spheres for left surface resampling > > <current-sphere> - a sphere with the same mesh as the current left > > surface > > <new-sphere> - a sphere with the new left mesh that is in register > > with the current sphere > > > > [-left-area-surfs] - specify left surfaces to do vertex area > > correction based on > > <current-area> - a relevant left anatomical surface with > current > > mesh > > <new-area> - a relevant left anatomical surface with new mesh > > > > [-left-area-metrics] - specify left vertex area metrics to do area > > correction based on > > <current-area> - a metric file with vertex areas for the > current > > mesh > > <new-area> - a metric file with vertex areas for the new mesh > > > > [-right-spheres] - specify spheres for right surface resampling > > <current-sphere> - a sphere with the same mesh as the current > right > > surface > > <new-sphere> - a sphere with the new right mesh that is in > register > > with the current sphere > > > > [-right-area-surfs] - specify right surfaces to do vertex area > > correction based on > > <current-area> - a relevant right anatomical surface with > current > > mesh > > <new-area> - a relevant right anatomical surface with new mesh > > > > [-right-area-metrics] - specify right vertex area metrics to do > area > > correction based on > > <current-area> - a metric file with vertex areas for the > current > > mesh > > <new-area> - a metric file with vertex areas for the new mesh > > > > [-cerebellum-spheres] - specify spheres for cerebellum surface > resampling > > <current-sphere> - a sphere with the same mesh as the current > > cerebellum surface > > <new-sphere> - a sphere with the new cerebellum mesh that is in > > register with the current sphere > > > > [-cerebellum-area-surfs] - specify cerebellum surfaces to do > vertex > > area correction based on > > <current-area> - a relevant cerebellum anatomical surface with > > current mesh > > <new-area> - a relevant cerebellum anatomical surface with new > mesh > > > > [-cerebellum-area-metrics] - specify cerebellum vertex area > metrics to > > do area correction based on > > <current-area> - a metric file with vertex areas for the > current > > mesh > > <new-area> - a metric file with vertex areas for the new mesh > > > > Resample cifti data to a different brainordinate space. Use COLUMN > for > > the direction to resample dscalar, dlabel, or dtseries. Resampling > both > > dimensions of a dconn requires running this command twice, once with > > COLUMN and once with ROW. If you are resampling a dconn and your > machine > > has a large amount of memory, you might consider using > > -cifti-resample-dconn-memory to avoid writing and rereading an > > intermediate file. If spheres are not specified for a surface > structure > > which exists in the cifti files, its data is copied without > resampling or > > dilation. Dilation is done with the 'nearest' method, and is done on > > <new-sphere> for surface data. Volume components are padded before > > dilation so that dilation doesn't run into the edge of the component > > bounding box. > > > > The recommended resampling methods are ADAP_BARY_AREA and CUBIC > (cubic > > spline), except for label data which should use ADAP_BARY_AREA and > > ENCLOSING_VOXEL. > > > > The <volume-method> argument must be one of the following: > > > > CUBIC > > ENCLOSING_VOXEL > > TRILINEAR > > > > The <surface-method> argument must be one of the following: > > > > ADAP_BARY_AREA > > BARYCENTRIC > > > > Best, > > Jenn > > > > Jennifer Elam, Ph.D. > Outreach Coordinator, Human Connectome Project > Washington University School of Medicine > Department of Anatomy and Neurobiology, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > [email protected] > www.humanconnectome.org > > > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *? > *Sent:* Thursday, October 29, 2015 3:15 AM > *To:* hcp-users > *Subject:* [HCP-Users] downsample > > > > hi, I have a question about downsample the fmri grayordinate data. > > 30k vertices means too many for me, I wander if I can find the > downsampled data from the database, if not, what should I do to downsample > using my own computer. > > Thank you. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
