Re: [Freesurfer] downsample fsnative

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On 2/26/19 11:33 AM, Ella Hanns wrote:

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Dear Bruce,

Thanks a lot for your help!

I now (roughly) ran the following pipeline but still did not manage to downsample my functional data in fsnative space:

1. /run mri_vol2surf to map functional data onto fsnative surface/:

My functional data contains one beta coefficient per voxel and represents a strong effect in auditory cortex regions. I see a similar pattern in volume and in surface space.

This the command I run:

mri_vol2surf --hemi $hemi \

--cortex \

--mov $data_path/sub-${subj}_volume_func.nii.gz \

--regheader sub-${subj} \

--out $data_path/sub-${subj}_surface_func _hemi-$hemi.gii \

--projfrac-avg 0.000 1.000 0.200 \

--trgsubject sub-${subj} \

--interp trilinear

2. /run mri_surf2surf to downsample functional data in fsnative space/:

The number of vertices in the downsampled sphere.reg file matches the number of vertices in the downsampled functional data but all I see when inspecting the data now is noise instead of auditory activation.

This is the command I run to downsample the sphere.reg file (downsampled file is stored in surf folder of dummy subject 99999):

mris_decimate -d 0.1 $data_path/surf/$hemi.sphere.reg $dummy_path/ surf/$hemi.sphere.reg

This is the command I run to downsample my functional data:

mri_surf2surf --hemi $hemi \

--srcsubject sub-${subj} \

--srcsurfval sub-${subj}_surface_func_hemi-$hemi.gii \

--trgsubject sub-99999 \

--trgsurfval sub-${subj}_surface_func_ds_hemi-$hemi.gii

Does anyone see what might go wrong here?

Any help would be greatly appreciated!

Cheers,

Ella

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