resampling of subcortical ROI

[Namrata Tamang]

Dear HCP team,

 I am working with subcortical ROIs  (CA1 and Subiculum-freesurfer seg) and would like to convert them into CIFTI space. I came across Tim’s note in a thread:

Following this, I attempted resampling using the command below:

wb_command -volume-resample   ca1_roi.nii   MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz ENCLOSING_VOXEL  ca1_roi_resampled.nii   \

 -warp T1w/BrainExtraction_FNIRTbased/str2standard.nii.gz   -fnirt T1w/T1w_acpc.nii.gz

Could you please confirm if this is the correct way to resample? I would like to confirm: whether the overall approach is correct and input files for <volume-space>, -warp, and -fnirt are appropriate. 

Thank you.

Best regards,

Namrata

[Tim Coalson]

I think our freesurfer space should be the same volume coordinates as our T1w rigid-aligned space (it is only their surface formats that have strange coordinates), which means the warp to get to MNINonLinear space is MNINonLinear/xfms/acpc_dc2standard.nii.gz .  That argument to -fnirt should be fine.  The 91k grayordinates use MNINonLinear space for the subcortical data.

You can use the ".nii.gz" extension for all your wb_command volume file outputs to save some disk space.

Tim

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[Namrata Tamang]

Dear Tim,

Thank you for you prompt reply!

Namrata

[Namrata Tamang]

Dear HCP team,

I have one more question, your guidance would be very helpful. I was able to compute CA1 and SUB connectivity maps using  -cifti-parcellate and  -cifti-cross-correlation for each ROIs.

 But, I would like to compute partial connectivity maps, e.g. CA1 connectivity while regressing out Subiculum’s time series (and vice versa). Is there a way to do this with Workbench commands, or would you recommend another approach?

Best regards,
Namrata 

[Glasser, Matthew]

You would need to do that in something like matlab or python.

Matt.

 

From: Namrata Tamang <namratat...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, September 17, 2025 at 8:22 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Namrata Tamang <namratat...@gmail.com>, "tim.c...@gmail.com" <tim.c...@gmail.com>
Subject: Re: [hcp-users] resampling of subcortical ROI

 

Dear HCP team,

I have one more question, your guidance would be very helpful. I was able to compute CA1 and SUB connectivity maps using  -cifti-parcellate and  -cifti-cross-correlation for each ROIs.

 But, I would like to compute partial connectivity maps, e.g. CA1 connectivity while regressing out Subiculum’s time series (and vice versa). Is there a way to do this with Workbench commands, or would you recommend another approach?

Best regards,
Namrata 

On Wednesday, September 3, 2025 at 1:59:57 PM UTC+9 Namrata Tamang wrote:

Dear Tim,

 

Thank you for you prompt reply!

Namrata

On Wednesday, September 3, 2025 at 1:47:54 PM UTC+9 Tim Coalson wrote:

I think our freesurfer space should be the same volume coordinates as our T1w rigid-aligned space (it is only their surface formats that have strange coordinates), which means the warp to get to MNINonLinear space is MNINonLinear/xfms/acpc_dc2standard.nii.gz .  That argument to -fnirt should be fine.  The 91k grayordinates use MNINonLinear space for the subcortical data.

 

You can use the ".nii.gz" extension for all your wb_command volume file outputs to save some disk space.

 

Tim

 

 

On Tue, Sep 2, 2025 at 11:15 PM Namrata Tamang <namratat...@gmail.com> wrote:

Dear HCP team,

 I am working with subcortical ROIs  (CA1 and Subiculum-freesurfer seg) and would like to convert them into CIFTI space. I came across Tim’s note in a thread:

Following this, I attempted resampling using the command below:

wb_command -volume-resample   ca1_roi.nii   MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz ENCLOSING_VOXEL  ca1_roi_resampled.nii   \

 -warp T1w/BrainExtraction_FNIRTbased/str2standard.nii.gz   -fnirt T1w/T1w_acpc.nii.gz

Could you please confirm if this is the correct way to resample? I would like to confirm: whether the overall approach is correct and input files for <volume-space>, -warp, and -fnirt are appropriate. 

Thank you.

Best regards,

Namrata

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