fsLR 32k - combining surfaces and subcortical data

[Ellyn Butler]

Hi HCP users,

I have some surface data in the fsLR 32k space, and am looking to combine it with subcortical data that is in MNI152NLin6Asym. I tried the following command as a first step: 

```

wb_command -cifti-create-dense-scalar \ ~/Documents/Northwestern/studies/mwmh/data/processed/neuroimaging/surf/sub-MWMH317/ses-1/func/sub-MWMH317_ses-1_task-rest_space-fsLR_desc-subcort_bold.dscalar.nii \

-volume ~/Documents/Northwestern/studies/mwmh/data/processed/neuroimaging/postproc/sub-MWMH317/ses-1/sub-MWMH317_ses-1_task-rest_space-MNI152NLin6Asym_desc-postproc_bold.nii.gz \

~/Documents/Northwestern/templates/Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors_with_Atlas_ROIs2.32k_fs_LR.dlabel.nii

```

but got the following error:

"ERROR: NAME OF FILE: Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors_with_Atlas_ROIs2.32k_fs_LR.dlabel.nii

PATH TO FILE: /Users/flutist4129/Documents/Northwestern/templates

Cifti files cannot be used as volume files"

What subcortical atlas should I be using? Or, is there a better way for me to be approaching this problem?

Best,

Ellyn

[Tim Coalson]

-cifti-create-dense-from-template is the easier command for this.  If you specifically want the 91k grayordinates space, I would recommend using the standard definition file as the template, the dscalar file here:

https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/91282_Greyordinates

However, cortical data needs to have already been mapped to the surface in order to put it into 91k grayordinates.  -volume-to-surface-mapping is the key step there.  The fMRIVolume and fMRISurface pipelines implement our recommended approach for preprocessing BOLD data and mapping it to the surface (and MR FIX to identify and remove motion-related and other artifacts).

Tim

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[Ellyn Butler]

Hi Tim,

Thank you! I tried running the following command:

```

wb_command -cifti-create-dense-from-template ~/Documents/Northwestern/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii \ ~/Documents/Northwestern/studies/mwmh/data/processed/neuroimaging/surf/sub-MWMH317/ses-1/func/sub-MWMH317_ses-1_task-rest_space-fsLR_desc-subcort_bold.dscalar.nii \

-volume-all ~/Documents/Northwestern/studies/mwmh/data/processed/neuroimaging/postproc/sub-MWMH317/ses-1/sub-MWMH317_ses-1_task-rest_space-MNI152NLin6Asym_desc-postproc_bold.nii.gz

```

And got the following error: "ERROR: -volume-all specifies a volume file that doesn't match the volume space of the template cifti file"

I am guessing that I have my MNI data in the wrong MNI space. Is that correct? If so, what is the correct MNI space (fMRIPrep parlance)?

https://www.templateflow.org/

Also, is there a way to use this command that would allow me to combine the subcortical volume data and the cortical surface data in one step?

Best,

Ellyn

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[Glasser, Matt]

We use FSL’s MNI space.

 

Matt.

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[Tim Coalson]

More precisely, our volume templates are here:

https://github.com/Washington-University/HCPpipelines/tree/master/global/templates

Resample to the 2mm version.  All the resolutions are aligned, including at a specific FoV corner, such that you can use FSL-convention transforms and tools to resample to the 2mm grid, using a warpfield derived from registering to the 0.7mm template (or any other combination).

Tim

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