Hi Matt,
1) I started from freesurfer results.
change FS surface and volume to gii or nii
2) create the white and pial surfaces with -surface-average
rh.white.gii lh.white.gii
3) surface mapping of fMR data with -volume-to-surface-mapping with -ribbon-constrained option (lh.white.gii lh.pial.gii)
4) make new surface (32k: Sphere.32k.L.surf.gii) with -surface-create-sphere
5) resampling to a lower resolution (32k) standard mesh with -metric-resample lh.func.gii lh.sphere.reg.surf.gii Sphere.32k.L.surf.gii ADAP_BARY_AREA lh.32k.func.gii
Then, I did subcortical process.
1) wmparc mgz (1*1*1mm) was resampled to MNI 2*2*2mm space
2) fMR volume also was resampled to this space
3) extracted subcortical labels from wmparc.2.nii.gz with -volume-label-import
Now I faced on difficulty in -volume-parcel-resampling
In wb_command -volume-parcel-resampling
I thought cur-parcels may be wmparc.2.nii.gz and new-parcels is the extracted subcortical labels from wmparc.2.nii.gz
But I faced on error message like below:
parcel volumes are not of type label
Could you check my process?
Thanks,
Jeong
----------------------------
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.
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