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Hi Doug,

Thank you for the explanation. It explains everything 😃

Cheers,

Dev

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Thursday, March 25, 2021 7:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol - Questions about label file and missing voxels?

On 3/23/2021 4:54 PM, Devavrat Vartak wrote:

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Hello freesurfer experts,

I am using mri_label2vol to convert my surface drawn label (of functional activity) to functional space (nifti) for more analysis (prf).

When I open the label file in text editor - it shows two lines at the top

#!ascii label , from subject vox2ras=TkReg

1287

1) Does the number 1287 represent selected voxels or does it represent something else?

It is the number of points in the label

I use the following command to convert:

mri_label2vol --subject sub-01 --hemi lh --label CustomLabel/lh.V1.label --regheader /sub-01/mri/orig.mgz --temp /sub-01/ses-1/mri_files/func_ref_file.nii.gz --o /prfdata/prfroi_mask/lh.V1.nii --fillthresh .3 --proj frac 0 1 .1

2) When I load the nifti file in python, I do not get 1287 voxels, I get only ~300 voxels. Why do I get so few voxels ?

You mean 300 active voxels, right? There should be as many voxels as in func_ref. Probably func_ref has a much larger voxels size, so there are fewer voxels.

Any help is appreciated.

Cheers,

Dev

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