Re: [HCP-Users] Subcortical surface sampling outside borders of CIFTI

[Glasser, Matthew]

I would map from volume to surface from the regular volume data without 
smoothing and then do the smoothing on the surface (which is what we do for the 
cerebral cortex).  What structures do you have surfaces of subcortically?

It might make the most sense to use the ICA+FIX cleaned data for this.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Reinder Vos de Wael 
<reinder.vosdew...@gmail.com<mailto:reinder.vosdew...@gmail.com>>
Date: Monday, April 17, 2017 at 12:05 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Subcortical surface sampling outside borders of CIFTI

Hi HCP,

I am extracting resting state data from subcortical surfaces. Initially, I had 
planned to do this based on the subcortical voxels included in the CIFTI file 
(i.e. rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii), however, some 
parts of my surfaces fall slightly outside the boundaries of grayordinate 
subcortical voxels. To resolve this, I tried sampling from the NIFTI file (i.e. 
rfMRI_REST1_LR_hp2000_clean.nii.gz), but I noticed that the voxels in the 
volumetric file don't necessarily contain the exact same timeseries as their 
counterparts in CIFTI.

As far as I have found in the HCP Pipeline code, the only difference between 
the NIFTI voxels and the CIFTI subcortical voxels is that the latter have 
undergone a parcel-based smoothing. Is this correct? If yes, should I resolve 
this by applying a parcel-based smooth on my slightly-deviating ROIs, run 
ICA-FIX, and sample from the resulting volume? If not, what would be the 
HCP-recommended way of dealing with this?

Many thanks,

Reinder

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[HCP-Users] Subcortical surface sampling outside borders of CIFTI

[Reinder Vos de Wael]

Hi HCP,

I am extracting resting state data from subcortical surfaces. Initially, I
had planned to do this based on the subcortical voxels included in the
CIFTI file (i.e. rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii),
however, some parts of my surfaces fall slightly outside the boundaries of
grayordinate subcortical voxels. To resolve this, I tried sampling from the
NIFTI file (i.e. rfMRI_REST1_LR_hp2000_clean.nii.gz), but I noticed that
the voxels in the volumetric file don't necessarily contain the exact same
timeseries as their counterparts in CIFTI.

As far as I have found in the HCP Pipeline code, the only difference
between the NIFTI voxels and the CIFTI subcortical voxels is that the
latter have undergone a parcel-based smoothing. Is this correct? If yes,
should I resolve this by applying a parcel-based smooth on my
slightly-deviating ROIs, run ICA-FIX, and sample from the resulting volume?
If not, what would be the HCP-recommended way of dealing with this?

Many thanks,

Reinder

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