You need to resample wmparc.nii.gz to whatever resolution you want the
subcortical data modeled at and then run this command:
wb_command -volume-label-import wmparc.${FinalfMRIResolution}.nii.gz
FreeSurferSubcorticalLabelTableLut.txt ROIs.${FinalfMRIResolution}.nii.gz
-discard-others
If you want to use the HCP standard 91282 grayordinates space, you should
download one of our subjects and use
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz
You don¡¯t want to use any -subvolume flag. Use the individual
parcellation (from the command above) as cur-parcels and the file I
mention from the HCP subject as new-parcels.
How did you downsample and achieve alignment on the surface? It might be
good to recount your steps so I can check them.
Peace,
Matt.
On 5/2/14, 1:41 AM, "SUBSCRIBE FSL B. Jeong" <[log in to unmask]> wrote:
>Hi Matt,
>
>Than you for your explanation.
>Now I've done surface mapping and resampling to a lower resolution
>standard mesh (32k) of fMR data using -surface-average,
>-volume-to-surface-mapping, and -metric-resample.
>
>Then, I'd like to subcortical processing for 4D fMR data.
>May be, I have to resample subcortical time series from individually
>defined greymatter nuclei to atlas defined nuclei, resulting in a
>standard set of subcortical voxels.
>According to help "wb_command -volume-parcel-resampling <vol-in>
><cur-parcels> <new-parcels> <kernel> <volume-out>", I'd like to type a
>command script like below,
>Sigma = 2
>wb_command -volume-parcel-resampling fmcpr.up.nii wmparc.nii.gz
><new-parcels> $Sigma R_thalmus.nii -subvolume 10
>
>What I don't know is,
>1) "wmparc.nii.gz" in mri directory of freesurfer result is the
><cur-parcels> or not?
>2) what is the <new-parcels> and how can I produce <new-parcels> file
>before performing the script above?
>3) Is it correct "-subvolume 10" for right thalamus? (when the value of
>label in wmparc.nii.gz is 10 for right thalamus)
>4) if so, there any way to make all <volume-out> files (thalamus,
>caudate, putamen ..... ) at once?
>
>Thanks,
>
>Jeong
>
>--------
>I do struggle a bit when the previous e-mails in a thread are not included
>below. You always want to be mapping data to the midthickness surface
>(which you can create by averaging the white and pial surfaces with
>wb_command -surface-average. Your output will be the <filename>.func.gii
>metric file containing the timeseries for one hemisphere (so you©öll need
>to get the other one from the other hemisphere). Ribbon-constrained
>mapping takes the white and pial surfaces, not the ribbon NIFTI file.
>
>Peace,
>
>Matt.
>
>On 4/29/14, 1:10 AM, "SUBSCRIBE FSL B. Jeong" <[log in to unmask]>
>wrote:
>
>>Hi Matt,
>>
>>Thank you for your kind explanation.
>>Unfortunately, I'm a newbie in terms of wb_command.
>>Could you kindly explain for me?
>>
>>If I have a 4D fMRI file ("fMR.nii.gz"), two freesurfer pial files
>>("lh.pial.gii", "rh.pial.gii"), and two freesurfer ribbon files
>>("rh.ribbon.nii.gz", "lh.ribbon.nii.gz"), what is the correct wb_command
>>script for mapping from fMR to surface space?
>>
>>The script below produced error message.
>>
>>wb_command -volume-to-surface-mapping fMR.nii.gz lh.pial.gii
>>output.dtseries.nii -ribbon-constrained lh.ribbon.nii.gz
>>
>>If -ribbon-constrained is replaced -trillinear, "output.dtseries.nii" was
>>produced. But workbench was not able to read it.
>>
>>Thanks,
>>
>>Jeong
>---------
>
>The exact process described in Glasser et al 2013 is a bit long as well
>and relies on previous pipelines for some things. The basic idea is
>volume to surface mapping with a ribbon-based approach (i.e. Define grey
>matter as the portion of voxels between the white and pial surface):
>
>wb_command -volume-to-surface-mapping
>
>Resampling to a lower resolution standard mesh (using a registered native
>mesh sphere), in this case a 32k mesh with 2mm average vertex spacing.
>
>wb_command -metric-resample
>
>Subcortical timeseries are resampled from individually defined grey matter
>nuclei (e.g. the thalamus) to atlas defined nuclei (making use of a prior
>nonlinear volume registration to achieve alignment), resulting in a
>standard set of subcortical voxels.
>
>wb_command -volume-parcel-resampling
>
>Then the standard surface data and standard subcortical data are combined
>into a dense timeseries
>
>wb_command -cifti-create-dense-timeseries
>
>Peace,
>
>Matt.
ACCUMBENS_LEFT
26 255 165 0 255
ACCUMBENS_RIGHT
58 255 165 0 255
AMYGDALA_LEFT
18 103 255 255 255
AMYGDALA_RIGHT
54 103 255 255 255
BRAIN_STEM
16 119 159 176 255
CAUDATE_LEFT
11 122 186 220 255
CAUDATE_RIGHT
50 122 186 220 255
CEREBELLUM_LEFT
8 230 148 34 255
CEREBELLUM_RIGHT
47 230 148 34 255
DIENCEPHALON_VENTRAL_LEFT
28 165 42 42 255
DIENCEPHALON_VENTRAL_RIGHT
60 165 42 42 255
HIPPOCAMPUS_LEFT
17 220 216 20 255
HIPPOCAMPUS_RIGHT
53 220 216 20 255
PALLIDUM_LEFT
13 12 48 255 255
PALLIDUM_RIGHT
52 13 48 255 255
PUTAMEN_LEFT
12 236 13 176 255
PUTAMEN_RIGHT
51 236 13 176 255
THALAMUS_LEFT
10 0 118 14 255
THALAMUS_RIGHT
49 0 118 14 255
|
