Cifti files are defined not only by their resolution, but also by ROIs that exclude uninteresting or redundant locations, in particular the medial wall vertices and white matter voxels for fMRI. This is the reason that -cifti-resample needs a template, to define what is included/excluded.
I'm not all that familiar with the HCP MEG data, and the outputs may not be in cifti format. You can get the cortical data from a cifti file in single-hemisphere gifti format using -cifti-separate, and you can use -metric-resample on those, which is a simpler command (because the gifti format does not have a provision for excluding vertices from the data file). You can also get the subcortical volume data using the same command, though for volume downsampling you should smooth before resampling in order not to waste signal (the volume resampling algorithms currently available in wb_command are point estimates, unlike the adaptive barycentric surface resampling). If the MEG data does provide cifti format files, you should be able to use any of them as the template in -cifti-resample, as I would expect them to all use the same defining ROIs. Tim On Tue, Jan 15, 2019 at 10:08 AM Rigel Wang < rigel.w...@neuroinformatics-collaboratory.org> wrote: > Hi Jan-Mathijs, > Thank you for your interest. > I want to resample the high spatial resolution fMRI signal to a low > spatial resolution to compare with the MEG signal in source space, which is > for comparing different M/EEG inverse methods. > So I want to convert the two modal signal in the same individual > coordinate system with low spatial resolution. > But I never did downsampling with HCP CIFTI file before. I want to use the > HCP Connectome Workbench command line to downsampling which can > avoid converting the format to other platforms for downsampling, such as > freesurfer -mri_surf2surf needs -reconall to segment T1w to their format > again then do downsampling. > However, the -cifti-resample <cfti-template> ask for CIFTI format file as > a target template. > I don't know what should it be. > I put the instruction description in the below. > Thank you! > Best, > Rigel > > > 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, > ROW or > COLUMN > <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, ROW or COLUMN > <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 or > popularity when doing surface resampling > > [-volume-predilate] - dilate the volume components before resampling > <dilate-mm> - distance, in mm, to dilate > > [-nearest] - use nearest value dilation > > [-weighted] - use weighted dilation (default) > > [-exponent] - specify exponent in weighting function > <exponent> - exponent 'n' to use in (1 / (distance ^ n)) > as the > weighting function (default 2) > > [-surface-postdilate] - dilate the surface components after resampling > <dilate-mm> - distance, in mm, to dilate > > [-nearest] - use nearest value dilation > > [-linear] - use linear dilation > > [-weighted] - use weighted dilation (default for non-label data) > > [-exponent] - specify exponent in weighting function > <exponent> - exponent 'n' to use in (area / (distance ^ > n)) as > the weighting function (default 2) > > [-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. The <template-direction> argument should > usually be > COLUMN, as dtseries, dscalar, and dlabel all have brainordinates on > that > direction. 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. If neither -affine nor -warpfield are specified, the > identity transform is assumed for the volume data. > > 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. Using ADAP_BARY_AREA requires specifying an area > option > to each used -*-spheres option. > > 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 > > > > From < > https://www.humanconnectome.org/software/workbench-command/-cifti-resample> > > > > > > ------------------------------ > *发件人:* Jan Mathijs Schoffelen <jm.schoffe...@gmail.com> > *发送时间:* 2019年1月15日 7:37 > *收件人:* Rigel Wang; HCP-Users@humanconnectome.org; Pedro Antonio > Valdés-Sosa; supp...@humanconnectome.org > *主题:* Re: [HCP-Users] 答复: About wb_command -cifti-resample > > Hi Rigel, > > I don’t see why you want to resample it, nor why it needs to be converted > into a cifti file. What’s your motivation for this? > Best wishes, > Jan-Mathijs > > > > On 15 Jan 2019, at 15:55, Rigel Wang < > rigel.w...@neuroinformatics-collaboratory.org> wrote: > > Hi Prof. Jan-Mathijs, > Thank you for your fast reply, this is very useful, I did not notice this > low-resolution source space anatomical file before. > Therefore, I need to convert this *.gii to CIFTI format as input to > -cifti-resample <cfti-template>? Or its corresponding MEG CIFTI data as > input to -cifti-resample <cfti-template>? > Vielen Dank > Best, > Rigel > > ------------------------------ > *发件人:* Schoffelen, J.M. (Jan Mathijs) <jan.schoffe...@donders.ru.nl> > *发送时间:* 2019年1月15日 6:41 > *收件人:* Rigel Wang; HCP-Users@humanconnectome.org > *抄送:* supp...@humanconnectome.org; Pedro Antonio Valdés-Sosa > *主题:* Re: [HCP-Users] About wb_command -cifti-resample > > Hi Rigel, > > I suggest to use the low resolution subject-specific source models, which > are part of the release data and are expressed in native space. > They exist in a 4k and 8k vertex-per-hemisphere version. See page 92 of > the S900 release manual. > > Best wishes, > Jan-Mathijs > > > On 15 Jan 2019, at 15:33, Rigel Wang < > rigel.w...@neuroinformatics-collaboratory.org> wrote: > > Hi HCP team, > Thanks a lot for your dedication to science. > I am using your HCP-S900 dataset and Connectome Workbench for research. > Specifically, in order to compare the E/MEG inverse solution, we are > expecting to get the low resolution resting state fMRI on native space > surface. > We are trying to use HCP-S900 dataset for a test. > > For example, we want to downsample the > *105923\MNINonLinear\Result\rfMRI_REST1_LR\rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii.* > > First, I use the wb_coomand -surface-resample in matlab to downsample > the anatomical data( > *system([wb_command, ' -surface-resample ',' ',file.highResSurface{hemi},' > ',file.highResSphere{hemi},' ',file.lowResSphere{hemi},' ', res_method,' > ',file.lowResSurface{hemi}]);)*for getting a low resolution suface which > expecting to be around 3k vertices for each hemisphere. PS: downsampling > the surface and projecting back to native space is for calculating the > E/MEG leadfied. > > *Then I am trying to use the wb_coomand -cifti-resample for downsample the > functional data(* > *system([wb_command, ' -cifti-resample ',' ',file.highResCii,' > ',res_src_direction,' ',cifti_templete,' ',res_template_direction,' > ',res_surface_method,' ', res_volume_method,' ',file.lowResCii]);) . * > > *Question:* > > 1. I don't know what should I put in the <cifti_templete> for wb_coomand > -cifti-resample? > > > 2. Can I use the same project matrix from > \105923\MNINonLinear\fsaverage_LR32k\105923.R.{pial or > white}.32k_fs_LR.surf.gii file, which is 4*4 matrix, for projecting > low-resolution 3k_fs_LR back, the output of -surface-resample, to > individual native space? > > > Thank you! > Best, > Rigel > > _______________________________________________ > 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 > Spam detection software, running on the system "mailman02.nrg.mir", has > identified this incoming email as possible spam. The original message > has been attached to this so you can view it (if it isn't spam) or label > similar future email. If you have any questions, see > @@CONTACT_ADDRESS@@ for details. > > Content preview: Hi Prof. Jan-Mathijs, Thank you for your fast reply, this > is very useful, I did not notice this low-resolution source space > anatomical > file before. Therefore, I need to convert this *.gii to CIFTI format as > input > to -cifti-resample <cfti-template>? Or its corresponding MEG CIFTI data > as > input to -cifti-resample <cfti-template>? Vielen Dank Best, Rigel [...] > > Content analysis details: (5.7 points, 5.0 required) > > pts rule name description > ---- ---------------------- > -------------------------------------------------- > 3.2 CHARSET_FARAWAY_HEADER A foreign language charset used in headers > 0.0 HTML_MESSAGE BODY: HTML included in message > 2.5 MIME_CHARSET_FARAWAY MIME character set indicates foreign language > 0.0 T_DKIM_INVALID DKIM-Signature header exists but is not valid > > > Spam detection software, running on the system "mailman02.nrg.mir", has > identified this incoming email as possible spam. The original message > has been attached to this so you can view it (if it isn't spam) or label > similar future email. If you have any questions, see > @@CONTACT_ADDRESS@@ for details. > > Content preview: Hi Prof. Jan-Mathijs, Thank you for your fast reply, this > is very useful, I did not notice this low-resolution source space > anatomical > file before. Therefore, I need to convert this *.gii to CIFTI format as > input > to -cifti-resample <cfti-template>? Or its corresponding MEG CIFTI data > as > input to -cifti-resample <cfti-template>? Vielen Dank Best, Rigel [...] > > Content analysis details: (5.7 points, 5.0 required) > > pts rule name description > ---- ---------------------- > -------------------------------------------------- > 3.2 CHARSET_FARAWAY_HEADER A foreign language charset used in headers > 0.0 HTML_MESSAGE BODY: HTML included in message > 2.5 MIME_CHARSET_FARAWAY MIME character set indicates foreign language > > > _______________________________________________ > 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
