External Email - Use Caution
Here is how I made the label into a surface overlay:
mri_label2vol --label $label/lh.7Networks_6.label --temp
/data/project/vislab/a/HCP_diff_Sara/fsaverage/mri/orig.mgz --identity --o
$vols/lh.7Networks_6.nii
mri_vol2surf --src $vols/lh.7Networks_6.nii --out $surfs/lh.7Networks_6.mgh
--regheader fsaverage --hemi lh
Here is the mri_mask command:
mri_mask betamaskedFPcflh.mgh $surfs/lh.7Networks_6.mgh
betasigandlabelmaskedFPcflh.mgh
Output from mri_mask:
DoAbs = 0
INFO: MRImask() using MRImaskDifferentGeometry()
Writing masked volume to betasigandlabelmaskedFPcflh.mgh...done.
Sara A. Sims, MA
Medical/Clinical Psychology Program
UAB | The University of Alabama at Birmingham
CIRC Suite 252A | 1719 6th Avenue South | Birmingham, AL 35294
P: 205.975.4060 | sno...@uab.edu
On 10/14/19, 2:35 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:
Hi Sara
we will need to know the actual commands and the screen output from them
that you ran
cheers
Bruce
On Mon, 14 Oct 2019, Sims, Sara A (Campus) wrote:
>
> External Email - Use Caution
>
> Freesurfers,
>
> I am trying to use mri_mask using surface overlays. I made a label into a
> volume and then into a surface with 1s inside the label and 0s outside the
> label. I want to make a connectivity map surface overlay with values only
> within my label overlay. However when I run it, it creates a surface
overlay
> with only zeros. There is definitely values within the label surface
overlay
> (I triple checked).
>
> Code I used:
>
> Mri_mask original_surface_overlay label_mask new_masked_output
>
>
>
> It doesn’t output any errors.
>
> Here is what it looks like in freeview:
>
> Original surface overlay (label is outlined in green)
>
> [IMAGE]
>
> The label made into a surface overlay (same as the one shown in green
> above):
>
> [IMAGE]
>
> But this is the output: all zeros even though there was data within the
> mask.
>
> [IMAGE]
>
>
>
> Help!
>
> Sara A. Sims
>
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
