Hi all, The shared MEG source reconstructed data are only defined on the cortical meshes, in cifti-format, and does not contain subcortical volumetrically defined brainordinates. Therefore, I suggest to go with Tim’s suggestion to do a cifti-separate on the fMRI ciftis and proceed from there. Best, Jan-Mathijs
> On 15 Jan 2019, at 20:55, Timothy Coalson <tsc...@mst.edu> wrote: > > 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 > <mailto: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 > <https://www.humanconnectome.org/software/workbench-command/-cifti-resample>> > > > > > 发件人: Jan Mathijs Schoffelen <jm.schoffe...@gmail.com > <mailto: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 > <mailto:HCP-Users@humanconnectome.org>; Pedro Antonio Valdés-Sosa; > supp...@humanconnectome.org <mailto: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 >> <mailto: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 >> <mailto: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 >> <mailto:HCP-Users@humanconnectome.org> >> 抄送: supp...@humanconnectome.org <mailto: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 >>> <mailto: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 >>> the105923\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 <mailto:HCP-Users@humanconnectome.org> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> <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 <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
