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<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
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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
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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
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to -cifti-resample <cfti-template>? Or its corresponding MEG CIFTI data as
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Content preview: 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 [...]
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