Thanks for getting back to me.
This is HCP data. Specifically, the social task. I am using FSL
(probtrackx) for tractography. I used the cifti-separate command and the
metric-resample command to extract the surface data. But I'm interested in
doing a whole-brain tractography with subcortical regions as well. So I
figured I could resample the surfaces to the fsaverage brain and then
combine them with the subcortical with vlrmerge. Do you have any other
recommendations on how I can get the output from cifti-separate into native
volume space?
Here are the commands I used:
# 1) Generate single-hemisphere gifti and volume nifti from cifti file
wb_command -cifti-separate-all ${contrast_dir}/zstat1.dtseries.nii \
-volume ${contrast_dir}/zstat.nii.gz \
-left ${contrast_dir}/zstat.L.func.gii \
-right ${contrast_dir}/zstat.R.func.gii
# 2) Map scalar data to fsaverage
for hemi in L R; do
wb_command -metric-resample \
${contrast_dir}/zstat.${hemi}.func.gii \
standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.${hemi}.sphere.32k_fs_LR.surf.gii
\
standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.${hemi}.164k_fsavg_${hemi}.surf.gii
ADAP_BARY_AREA \
${contrast_dir}/${hemi}.164k_fsavg_${hemi}.func.gii \
-area-metrics
standard_mesh_atlases/resample_fsaverage/fs_LR.${hemi}.midthickness_va_avg.32k_fs_LR.shape.gii
\
standard_mesh_atlases/resample_fsaverage/fsaverage.${hemi}.midthickness_va_avg.164k_fsavg_${hemi}.shape.gii
done
# Register subcortical data to MNI305
mri_vol2vol --mov ${contrast_dir}/zstat.nii.gz \
--targ
/usr/local/freesurfer/subjects/fsaverage/mri.2mm/mni305.cor.mgz \
--xfm $SUBJECTS_DIR/${SUB}/mri/transforms/talairach.xfm \
--o ${contrast_dir}/zstat.mni305.2mm.nii.gz
# Merge surface data with subcortical into one combined volume
vlrmerge --o ${contrast_dir}/zstat_combined.nii.gz \
--lh ${contrast_dir}/L.164k_fsavg_L.func.gii \
--rh ${contrast_dir}/R.164k_fsavg_R.func.gii \
--v ${contrast_dir}/zstat.mni305.2mm.nii.gz \
--scm /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz
On Thu, Apr 4, 2019 at 9:32 PM Glasser, Matthew <glass...@wustl.edu> wrote:
> Is this HCP data? What software are you using for tractography? If you
> want statistical maps in native volume space, it might be easiest to
> project them from the subject’s physical space surfaces in the
> T1w/fsaverage_LR32k or alternatively track the data to those surfaces.
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Haroon Popal <
> tuk12...@temple.edu>
> Date: Wednesday, April 3, 2019 at 5:15 PM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] Standard to Native Applywarp Error
>
> Hello,
>
> I am trying to use the provided commands in the link below to transform a
> contrast from the social task to native space.
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-16.CanIgetthefMRIdatainasubject's'nativespace'?
>
> I used the pipeline in the second link to extract the surface and
> subcortical data from the original zstat.dtseries.nii file in one of the
> cope directories. I then used vlrmerge from FreeSurfer to combine the
> surface and volume data.
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?
>
> When I run the applywarp command, I'm getting a weird registration, where
> the brain is tilted up in the sagittal view, with the frontal lobe of the
> functional data pointing upwards.
>
> I am trying to do all of these because I need a volume for the contrast
> map, to compare to some DTI. I need my functional data and DTI data in the
> same space.
>
> Thanks for your help.
>
> --
> Haroon S. Popal
> Ph.D. Student
> Cognitive Neuroscience Laboratory
> Department of Psychology | Temple University
>
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> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
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--
Haroon S. Popal
Ph.D. Student
Cognitive Neuroscience Laboratory
Department of Psychology | Temple University
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