Re: [Freesurfer] Mri_mask producing only zeros

[Greve, Douglas N.,Ph.D.]

Can you send the full terminal output?

On 10/14/19 12:01 AM, 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)
>
> The label made into a surface overlay (same  as the one shown in green 
> above):
>
> But this is the output: all zeros even though there was data within 
> the mask.
>
> Help!
>
> *Sara A. Sims*
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Mri_mask producing only zeros

[Greve, Douglas N.,Ph.D.]

Can you send the full command line (the one below does not make sense)? And 
send the terminal output

On 10/14/19 11:53 AM, 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.
Sara A. Sims




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Mri_mask producing only zeros

[Sims, Sara A (Campus)]

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"  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

Re: [Freesurfer] Mri_mask producing only zeros

[Bruce Fischl]

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

[Freesurfer] Mri_mask producing only zeros

[Sims, Sara A (Campus)]

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.
Sara A. Sims

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer