Re: [Freesurfer] mri_mask error exits returns a zero exit status

[Douglas N. Greve]

yes, you are correct. I just fixed that, so it will be in the next release.

On 1/10/2023 4:14 PM, Aaron Tanenbaum wrote:


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I should have said I am using FS 7.3 on Ubuntu 20.04

On Tue, Jan 10, 2023 at 12:23 PM Aaron Tanenbaum 
 wrote:


Hello,
FYI, I recently noticed that mri_mask returns a zero exit status
when it is unable to write the output.


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Re: [Freesurfer] mri_mask error exits returns a zero exit status

[fsbuild]

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Just curious what output (if any) is echoed to the terminal when the failure 
occurs.

- R.

On Jan 10, 2023, at 13:23, Aaron Tanenbaum aaron.b.tanenb...@gmail.com 
wrote:External Email - Use 
CautionHello,FYI, I recently 
noticed that mri_mask returns a zero exit status when it is unable to write the 
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Re: [Freesurfer] mri_mask error exits returns a zero exit status

[Aaron Tanenbaum]

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I should have said I am using FS 7.3 on Ubuntu 20.04

On Tue, Jan 10, 2023 at 12:23 PM Aaron Tanenbaum <
aaron.b.tanenb...@gmail.com> wrote:

> Hello,
> FYI, I recently noticed that mri_mask returns a zero exit status when it
> is unable to write the output.
>
>
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[Freesurfer] mri_mask error exits returns a zero exit status

[Aaron Tanenbaum]

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Hello,
FYI, I recently noticed that mri_mask returns a zero exit status when it is
unable to write the output.
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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*
>
>
> ___
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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:

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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




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Re: [Freesurfer] Mri_mask producing only zeros

[Sims, Sara A (Campus)]

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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
> 
>  
> 
> 
>


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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

 


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[Freesurfer] Mri_mask producing only zeros

[Sims, Sara A (Campus)]

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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

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[Freesurfer] mri_mask output problem

[Caspar M. Schwiedrzik]

Hi Freesurfer Experts,
I am trying to apply a mask that I made with FSL's bet to a NIFTI file that
I got from someone else.
The mask looks fine, the NIFTI file is in float format, does not contain
NaNs or negative values, but the overall values are all pretty low (in the
40ies). When I try to apply the mask to the NIFTI file using mri_mask, the
output I get is essentially a copy of the mask (only zeros and ones). The
same happens if I use fslmaths.
Any advice would be very much appreciated.
Thanks, Caspar
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Re: [Freesurfer] mri_mask output problem

[Douglas Greve]

what is your command line and terminal output?


On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:

Hi Freesurfer Experts,
I am trying to apply a mask that I made with FSL's bet to a NIFTI file 
that I got from someone else.
The mask looks fine, the NIFTI file is in float format, does not 
contain NaNs or negative values, but the overall values are all pretty 
low (in the 40ies). When I try to apply the mask to the NIFTI file 
using mri_mask, the output I get is essentially a copy of the mask 
(only zeros and ones). The same happens if I use fslmaths.

Any advice would be very much appreciated.
Thanks, Caspar



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Re: [Freesurfer] mri_mask output problem

[Caspar M. Schwiedrzik]

Hi Doug,
this is the command line input:
mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz
macaque_stripped_final2.nii
this is the terminal output:
DoAbs = 0
Found 14652800 voxels in mask
Writing masked volume to macaque_stripped_final2.nii...done.
The same thing happens when I use nii.gz or mgz files.

Caspar



2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu


 what is your command line and terminal output?



 On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:

   Hi Freesurfer Experts,
  I am trying to apply a mask that I made with FSL's bet to a NIFTI file
 that I got from someone else.
  The mask looks fine, the NIFTI file is in float format, does not contain
 NaNs or negative values, but the overall values are all pretty low (in the
 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the
 output I get is essentially a copy of the mask (only zeros and ones). The
 same happens if I use fslmaths.
  Any advice would be very much appreciated.
  Thanks, Caspar



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 e-mail
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 HelpLine at
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Re: [Freesurfer] mri_mask output problem

[Douglas Greve]

And macaque_25_model-MNI.nii is the non-binary image? And 
macaque_stripped_mask.nii.gz is the binary mask? If so, the command 
looks right to me.

doug

On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
this is the command line input:
mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz 
macaque_stripped_final2.nii

this is the terminal output:
DoAbs = 0
Found 14652800 voxels in mask
Writing masked volume to macaque_stripped_final2.nii...done.
The same thing happens when I use nii.gz or mgz files.

Caspar



2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu



what is your command line and terminal output?



On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:

Hi Freesurfer Experts,
I am trying to apply a mask that I made with FSL's bet to a NIFTI
file that I got from someone else.
The mask looks fine, the NIFTI file is in float format, does not
contain NaNs or negative values, but the overall values are all
pretty low (in the 40ies). When I try to apply the mask to the
NIFTI file using mri_mask, the output I get is essentially a copy
of the mask (only zeros and ones). The same happens if I use
fslmaths.
Any advice would be very much appreciated.
Thanks, Caspar



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Re: [Freesurfer] mri_mask output problem

[Caspar M. Schwiedrzik]

Hi Doug,
that's correct.
I think the problem is perhaps that the original NIFTI file has a very
narrow range of values, between 43.7308 and 43.8476, to cover the whole
range of tissues in the image.
It is an average over several subjects, and before skull stripping, there
are hardly any zeros in the image.
Is there a way to rescale the file?
Thanks, Caspar




2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu

  And macaque_25_model-MNI.nii is the non-binary image? And
 macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks
 right to me.
 doug


 On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote:

  Hi Doug,
 this is the command line input:
 mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz
 macaque_stripped_final2.nii
 this is the terminal output:
 DoAbs = 0
 Found 14652800 voxels in mask
 Writing masked volume to macaque_stripped_final2.nii...done.
  The same thing happens when I use nii.gz or mgz files.

  Caspar



 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu


 what is your command line and terminal output?



 On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:

Hi Freesurfer Experts,
  I am trying to apply a mask that I made with FSL's bet to a NIFTI file
 that I got from someone else.
  The mask looks fine, the NIFTI file is in float format, does not contain
 NaNs or negative values, but the overall values are all pretty low (in the
 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the
 output I get is essentially a copy of the mask (only zeros and ones). The
 same happens if I use fslmaths.
  Any advice would be very much appreciated.
  Thanks, Caspar



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Re: [Freesurfer] mri_mask output problem

[Douglas Greve]

That should not be a problem. Certainly it should not cause everything 
to go to 1s and 0s. What version of FS are you using? And you say the 
same thing happens with FSL? Try using mri_convert to convert the 
nonbinary image to another nifti file and see if you get 1s and 0s. If 
not, then try that file as input. You can also try fscalc, something like


fscalc input.nii mul mask.nii -o output.nii

should accomplish the same thing

doug




On 12/30/13 1:12 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
that's correct.
I think the problem is perhaps that the original NIFTI file has a very 
narrow range of values, between 43.7308 and 43.8476, to cover the 
whole range of tissues in the image.
It is an average over several subjects, and before skull stripping, 
there are hardly any zeros in the image.

Is there a way to rescale the file?
Thanks, Caspar




2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu


And macaque_25_model-MNI.nii is the non-binary image? And
macaque_stripped_mask.nii.gz is the binary mask? If so, the
command looks right to me.
doug


On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
this is the command line input:
mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz
macaque_stripped_final2.nii
this is the terminal output:
DoAbs = 0
Found 14652800 voxels in mask
Writing masked volume to macaque_stripped_final2.nii...done.
The same thing happens when I use nii.gz or mgz files.

Caspar



2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu


what is your command line and terminal output?



On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:

Hi Freesurfer Experts,
I am trying to apply a mask that I made with FSL's bet to a
NIFTI file that I got from someone else.
The mask looks fine, the NIFTI file is in float format, does
not contain NaNs or negative values, but the overall values
are all pretty low (in the 40ies). When I try to apply the
mask to the NIFTI file using mri_mask, the output I get is
essentially a copy of the mask (only zeros and ones). The
same happens if I use fslmaths.
Any advice would be very much appreciated.
Thanks, Caspar



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sent to you in error
but does not contain patient information, please contact the
sender and properly
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_mask output problem

[Caspar M. Schwiedrzik]

Hi Doug,
thanks for your input. I turns out that there is some problem when
converting minc to NIFTI with float. I got a hold of the original minc file
and converted it to NIFTI with minc2nii using integer, and now the values
are in a reasonable range and the skull stripping works.
Thanks!
Caspar



2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu


 That should not be a problem. Certainly it should not cause everything to
 go to 1s and 0s. What version of FS are you using? And you say the same
 thing happens with FSL? Try using mri_convert to convert the nonbinary
 image to another nifti file and see if you get 1s and 0s. If not, then try
 that file as input. You can also try fscalc, something like

 fscalc input.nii mul mask.nii -o output.nii

 should accomplish the same thing

 doug





 On 12/30/13 1:12 PM, Caspar M. Schwiedrzik wrote:

  Hi Doug,
 that's correct.
  I think the problem is perhaps that the original NIFTI file has a very
 narrow range of values, between 43.7308 and 43.8476, to cover the whole
 range of tissues in the image.
 It is an average over several subjects, and before skull stripping, there
 are hardly any zeros in the image.
 Is there a way to rescale the file?
  Thanks, Caspar




 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu

  And macaque_25_model-MNI.nii is the non-binary image? And
 macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks
 right to me.
 doug


 On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote:

  Hi Doug,
 this is the command line input:
 mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz
 macaque_stripped_final2.nii
 this is the terminal output:
 DoAbs = 0
 Found 14652800 voxels in mask
 Writing masked volume to macaque_stripped_final2.nii...done.
  The same thing happens when I use nii.gz or mgz files.

  Caspar



 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu


 what is your command line and terminal output?



 On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:

Hi Freesurfer Experts,
  I am trying to apply a mask that I made with FSL's bet to a NIFTI file
 that I got from someone else.
  The mask looks fine, the NIFTI file is in float format, does not
 contain NaNs or negative values, but the overall values are all pretty low
 (in the 40ies). When I try to apply the mask to the NIFTI file using
 mri_mask, the output I get is essentially a copy of the mask (only zeros
 and ones). The same happens if I use fslmaths.
  Any advice would be very much appreciated.
  Thanks, Caspar



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


 The information in this e-mail is intended only for the person to whom
 it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.






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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_mask problem

[Gabriel Go.Es.]

That works!!!

Thank you,
Gabriel

 





 Date: Tue, 15 Mar 2011 14:34:00 -0400
 From: gr...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; 
 ni...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mri_mask problem
 
 For mri_vol2vol try using --interp nearest
 doug
 
 Gabriel Go.Es. wrote:
 
  Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or 
  brainmask2raw.gz to mask the rawavg.gz on the mri_mask. mri_mask -T 2 
  -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz
  And actually the brain.mgz and brainmask.mgz have values of one on 
  edited voxels, but after mri_vol2vol or mri_convert -rl the voxel 
  values appear with bigger values, and some of these values are like 
  ventricles values, so I can not just put a high threshold; new values  
  on edited voxels range from 1 to 40 approximately, and yes, the 
  background has values less than 2.
  Gabriel
 
 
 
 
 
   Date: Tue, 15 Mar 2011 13:30:40 -0400
   From: gr...@nmr.mgh.harvard.edu
   To: gabriel...@hotmail.com
   CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; 
  ni...@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] mri_mask problem
  
   Have you checked brainmask2raw.mgz? It looks like you've checked
   brain2raw.mgz, but you're not using it for some reason. Make sure the
   background has values less than 2.
   doug
  
   Gabriel Go.Es. wrote:
   
Hello Bruce and Nick, I've tryed these options you said and still not
works, I must say that is not in all my subjects,
   
I've tryed both brain.mgz and brainmask.mgz.
   
The commands I've used are:
   
A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
brain2raw.mgz --regheader
A2) mri_mask flag -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz
outbrain.mgz
   
after mri_vol2vol the brain2raw.mgz look perfecty fine, but when
apply the mri_mask the image apperars with no edits.
   
B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz
B2) mri_mask flag -T 2 -keep_mask_deletion_edits rawavg.mgz
brainmask2raw.mgz outbrain2.mgz
   
I've ran the mri_mask command with and without the
-keep_mask_deletion_edits flag
and again appears to be the mri_mask command the one that is not 
  doing
the work, actually the outputs from mri_convert and mri_vol2vol, 
  looks
pretty similar, any ideas?
   
Bests
Gabriel
   
   
   
   
   
 Date: Mon, 14 Mar 2011 08:57:16 -0400
 From: fis...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mri_mask problem

 Hi Gabriel,

 did you convert the brain.mgz so it is in the same space as the
 rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you
can try
 mri_mask -t threshold. The default is 1e-10 so pretty much 
  anything
 non-zero is dept. Try changing it to 2 (voxels edited to be turned
off are
 1).

 cheers
 Bruce

 On Mon, 14 Mar 2011,
 Gabriel Go.Es. wrote:

 
  Hello Nick
 
  I'm wondering if you're able to verify my data today,
  I did try using brainmask.mgz to mask the rawavg.mgz, and didn't
worked,
  I'm guessing you'll need my data, to see if there is something
wrong on it, but I think is gonna be hard to send it to through the
e-mail.
 
  Bests,
  Gabriel.
 
 
 
  Subject: RE: [Freesurfer] mri_mask problem
  From: ni...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  Date: Thu, 10 Mar 2011 21:38:50 -0500
 
  i'd have to try to replicate this myself, although it will have
to wait
  till monday (i'm with the freesurfer group three days a week).
 
  i wonder if you can use the brain.mgz as your mask instead of
  brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels 
  but
their
  actually not there (zeroed).
 
  n.
 
  On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
  Hello Nick,
  good mornig for you, when you read this, Now I have tryed the
flag in
  the mri_mask command but it seems too similar to what was doing
  before, it says that will transfer 1 voxel edits to dst vol, 
  but
there
  many more voxels edited, I have also tryed mri_vol2vol in the
  brainmask.mgz intead of brain.mgz but the result is exactly 
  the same
  (the output from mri_vol2vol has the voxel 'deletions', but the
  mri_mask ignore them. Now i have no idea how to solve this, 
  do you?
 
  Bests,
  Gabriel
 
 
 
 
 
 
 
  Subject: RE: [Freesurfer] mri_mask problem
  From: ni...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  Date: Wed, 9 Mar 2011 18:00:37 -0500
 
  we've improved some of the help text for the next version 
  (5.1),
  which

Re: [Freesurfer] mri_mask problem

[Gabriel Go.Es.]

Hello Bruce and Nick, I've tryed these options you said and still not works, I 
must say that is not in all my subjects,

 

I've tryed both brain.mgz and brainmask.mgz.
 
The commands I've used are:


A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz 
--regheader
A2) mri_mask flag -keep_mask_deletion_edits  rawavg.mgz brain2raw.mgz 
outbrain.mgz

 

after mri_vol2vol the brain2raw.mgz look perfecty fine, but when apply the 
mri_mask the image apperars with no edits. 


B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz

B2) mri_mask flag -T 2 -keep_mask_deletion_edits  rawavg.mgz brainmask2raw.mgz 
outbrain2.mgz

 

I've ran the mri_mask command with and without the -keep_mask_deletion_edits 
flag
and again appears to be the mri_mask command the one that is not doing the 
work, actually the outputs from mri_convert and mri_vol2vol, looks pretty 
similar, any ideas?

 

Bests

Gabriel


 

 


 

 Date: Mon, 14 Mar 2011 08:57:16 -0400
 From: fis...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mri_mask problem
 
 Hi Gabriel,
 
 did you convert the brain.mgz so it is in the same space as the 
 rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try 
 mri_mask -t threshold. The default is 1e-10 so pretty much anything 
 non-zero is dept. Try changing it to 2 (voxels edited to be turned off are 
 1).
 
 cheers
 Bruce
 
 On Mon, 14 Mar 2011, 
 Gabriel Go.Es. wrote:
 
 
  Hello Nick
 
  I'm wondering if you're able to verify my data today,
  I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
  I'm guessing you'll need my data, to see if there is something wrong on it, 
  but I think is gonna be hard to send it to through the e-mail.
 
  Bests,
  Gabriel.
 
 
 
  Subject: RE: [Freesurfer] mri_mask problem
  From: ni...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  Date: Thu, 10 Mar 2011 21:38:50 -0500
 
  i'd have to try to replicate this myself, although it will have to wait
  till monday (i'm with the freesurfer group three days a week).
 
  i wonder if you can use the brain.mgz as your mask instead of
  brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
  actually not there (zeroed).
 
  n.
 
  On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
  Hello Nick,
  good mornig for you, when you read this, Now I have tryed the flag in
  the mri_mask command but it seems too similar to what was doing
  before, it says that will transfer 1 voxel edits to dst vol, but there
  many more voxels edited, I have also tryed mri_vol2vol in the
  brainmask.mgz intead of brain.mgz but the result is exactly the same
  (the output from mri_vol2vol has the voxel 'deletions', but the
  mri_mask ignore them. Now i have no idea how to solve this, do you?
 
  Bests,
  Gabriel
 
 
 
 
 
 
 
  Subject: RE: [Freesurfer] mri_mask problem
  From: ni...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  Date: Wed, 9 Mar 2011 18:00:37 -0500
 
  we've improved some of the help text for the next version (5.1),
  which
  is the only reason i noticed it this time.
 
 
  On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
 
  Than you Nick,
 
  Actually that was exactly what i did, delete some voxels from the
  brainmask, I will try adding the flag and let you know, I dind't
  saw
  that this option exist in the mri_mask.
 
  thank you again,
  Gabriel
 
 
 
 
 
 
  Subject: Re: [Freesurfer] mri_mask problem
  From: ni...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  CC: freesurfer@nmr.mgh.harvard.edu
  Date: Wed, 9 Mar 2011 17:52:34 -0500
 
  hi, not sure what you are trying to do, as the commands below
  seem
  to do
  what i expect them to do, which is to create a masked
  (skull-stripped)
  version of rawavg.mgz. what do you mean by 'manual segmentation
  changes'?, and what exactly is going wrong?
 
  if you deleted voxels in brainmask.mgz, then perhaps you need to
  add
  the
  flag -keep_mask_deletion_edits to mri_mask to transfer those
  voxels
  ('deleted' voxels actually have a special value to indicate
  deleted).
 
  n.
 
 
 
  On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
 
  Hello everybody,
  Sorry for the insistance, but I need to solve this...
 
  I'm making some manual segmentation changes in the
  brainmask.mgz
  and
  using mri_vol2vol and mri_mask commands to apply these changes
  to
  the
  rawavg.mgz, the output from the mri_vol2vol looks perfectly
  normal,and
  retains all changed made by me, but when I use the mri_mask
  command
  over the rawavg.mgz no segmentation seems to be donne in the
  final
  output file.
 
 
  Does any one has an idea of what could be wrong?
 
 
  the commands after manual corrections are:
 
 
  mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
  brain2raw.mgz
  --regheader
  mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
 
 
 
 
  Thanks in advanced,
  Gabriel

Re: [Freesurfer] mri_mask problem

[Douglas N Greve]

Have you checked brainmask2raw.mgz? It looks like you've checked 
brain2raw.mgz, but you're not using it for some reason. Make sure the 
background has values less than 2.
doug

Gabriel Go.Es. wrote:

 Hello Bruce and Nick, I've tryed these options you said and still not 
 works, I must say that is not in all my subjects,
  
 I've tryed both brain.mgz and brainmask.mgz.
  
 The commands I've used are:

 A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out 
 brain2raw.mgz --regheader
 A2) mri_mask flag -keep_mask_deletion_edits  rawavg.mgz brain2raw.mgz 
 outbrain.mgz
  
 after mri_vol2vol the brain2raw.mgz look perfecty fine, but when 
 apply the mri_mask the image apperars with no edits.

 B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz
 B2) mri_mask flag -T 2 -keep_mask_deletion_edits  rawavg.mgz 
 brainmask2raw.mgz outbrain2.mgz
  
 I've ran the mri_mask command with and without the 
 -keep_mask_deletion_edits flag
 and again appears to be the mri_mask command the one that is not doing 
 the work, actually the outputs from mri_convert and mri_vol2vol, looks 
 pretty similar, any ideas?
  
 Bests
 Gabriel

  
  

  
  Date: Mon, 14 Mar 2011 08:57:16 -0400
  From: fis...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] mri_mask problem
 
  Hi Gabriel,
 
  did you convert the brain.mgz so it is in the same space as the
  rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you 
 can try
  mri_mask -t threshold. The default is 1e-10 so pretty much anything
  non-zero is dept. Try changing it to 2 (voxels edited to be turned 
 off are
  1).
 
  cheers
  Bruce
 
  On Mon, 14 Mar 2011,
  Gabriel Go.Es. wrote:
 
  
   Hello Nick
  
   I'm wondering if you're able to verify my data today,
   I did try using brainmask.mgz to mask the rawavg.mgz, and didn't 
 worked,
   I'm guessing you'll need my data, to see if there is something 
 wrong on it, but I think is gonna be hard to send it to through the 
 e-mail.
  
   Bests,
   Gabriel.
  
  
  
   Subject: RE: [Freesurfer] mri_mask problem
   From: ni...@nmr.mgh.harvard.edu
   To: gabriel...@hotmail.com
   Date: Thu, 10 Mar 2011 21:38:50 -0500
  
   i'd have to try to replicate this myself, although it will have 
 to wait
   till monday (i'm with the freesurfer group three days a week).
  
   i wonder if you can use the brain.mgz as your mask instead of
   brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but 
 their
   actually not there (zeroed).
  
   n.
  
   On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
   Hello Nick,
   good mornig for you, when you read this, Now I have tryed the 
 flag in
   the mri_mask command but it seems too similar to what was doing
   before, it says that will transfer 1 voxel edits to dst vol, but 
 there
   many more voxels edited, I have also tryed mri_vol2vol in the
   brainmask.mgz intead of brain.mgz but the result is exactly the same
   (the output from mri_vol2vol has the voxel 'deletions', but the
   mri_mask ignore them. Now i have no idea how to solve this, do you?
  
   Bests,
   Gabriel
  
  
  
  
  
  
  
   Subject: RE: [Freesurfer] mri_mask problem
   From: ni...@nmr.mgh.harvard.edu
   To: gabriel...@hotmail.com
   Date: Wed, 9 Mar 2011 18:00:37 -0500
  
   we've improved some of the help text for the next version (5.1),
   which
   is the only reason i noticed it this time.
  
  
   On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
  
   Than you Nick,
  
   Actually that was exactly what i did, delete some voxels from the
   brainmask, I will try adding the flag and let you know, I dind't
   saw
   that this option exist in the mri_mask.
  
   thank you again,
   Gabriel
  
  
  
  
  
  
   Subject: Re: [Freesurfer] mri_mask problem
   From: ni...@nmr.mgh.harvard.edu
   To: gabriel...@hotmail.com
   CC: freesurfer@nmr.mgh.harvard.edu
   Date: Wed, 9 Mar 2011 17:52:34 -0500
  
   hi, not sure what you are trying to do, as the commands below
   seem
   to do
   what i expect them to do, which is to create a masked
   (skull-stripped)
   version of rawavg.mgz. what do you mean by 'manual segmentation
   changes'?, and what exactly is going wrong?
  
   if you deleted voxels in brainmask.mgz, then perhaps you need to
   add
   the
   flag -keep_mask_deletion_edits to mri_mask to transfer those
   voxels
   ('deleted' voxels actually have a special value to indicate
   deleted).
  
   n.
  
  
  
   On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
  
   Hello everybody,
   Sorry for the insistance, but I need to solve this...
  
   I'm making some manual segmentation changes in the
   brainmask.mgz
   and
   using mri_vol2vol and mri_mask commands to apply these changes
   to
   the
   rawavg.mgz, the output from the mri_vol2vol looks perfectly
   normal,and
   retains all changed made by me, but when I use the mri_mask
   command
   over the rawavg.mgz

Re: [Freesurfer] mri_mask problem

[Gabriel Go.Es.]

Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or 
brainmask2raw.gz to mask the rawavg.gz on the mri_mask.  mri_mask -T 2 
-keep_mask_deletion_edits  rawavg.mgz brain2raw.mgz outbrain.mgz
And actually the brain.mgz and brainmask.mgz have values of one on edited 
voxels, but after mri_vol2vol or mri_convert -rl the voxel values appear with 
bigger values, and some of these values are like ventricles values, so I can 
not just put a high threshold; new values  on edited voxels range from 1 to 40 
approximately, and yes, the background has values less than 2.
Gabriel





 Date: Tue, 15 Mar 2011 13:30:40 -0400
 From: gr...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; 
 ni...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mri_mask problem
 
 Have you checked brainmask2raw.mgz? It looks like you've checked 
 brain2raw.mgz, but you're not using it for some reason. Make sure the 
 background has values less than 2.
 doug
 
 Gabriel Go.Es. wrote:
 
  Hello Bruce and Nick, I've tryed these options you said and still not 
  works, I must say that is not in all my subjects,
   
  I've tryed both brain.mgz and brainmask.mgz.
   
  The commands I've used are:
 
  A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out 
  brain2raw.mgz --regheader
  A2) mri_mask flag -keep_mask_deletion_edits  rawavg.mgz brain2raw.mgz 
  outbrain.mgz
   
  after mri_vol2vol the brain2raw.mgz look perfecty fine, but when 
  apply the mri_mask the image apperars with no edits.
 
  B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz
  B2) mri_mask flag -T 2 -keep_mask_deletion_edits  rawavg.mgz 
  brainmask2raw.mgz outbrain2.mgz
   
  I've ran the mri_mask command with and without the 
  -keep_mask_deletion_edits flag
  and again appears to be the mri_mask command the one that is not doing 
  the work, actually the outputs from mri_convert and mri_vol2vol, looks 
  pretty similar, any ideas?
   
  Bests
  Gabriel
 
   
   
 
   
   Date: Mon, 14 Mar 2011 08:57:16 -0400
   From: fis...@nmr.mgh.harvard.edu
   To: gabriel...@hotmail.com
   CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] mri_mask problem
  
   Hi Gabriel,
  
   did you convert the brain.mgz so it is in the same space as the
   rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you 
  can try
   mri_mask -t threshold. The default is 1e-10 so pretty much anything
   non-zero is dept. Try changing it to 2 (voxels edited to be turned 
  off are
   1).
  
   cheers
   Bruce
  
   On Mon, 14 Mar 2011,
   Gabriel Go.Es. wrote:
  
   
Hello Nick
   
I'm wondering if you're able to verify my data today,
I did try using brainmask.mgz to mask the rawavg.mgz, and didn't 
  worked,
I'm guessing you'll need my data, to see if there is something 
  wrong on it, but I think is gonna be hard to send it to through the 
  e-mail.
   
Bests,
Gabriel.
   
   
   
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Thu, 10 Mar 2011 21:38:50 -0500
   
i'd have to try to replicate this myself, although it will have 
  to wait
till monday (i'm with the freesurfer group three days a week).
   
i wonder if you can use the brain.mgz as your mask instead of
brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but 
  their
actually not there (zeroed).
   
n.
   
On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
Hello Nick,
good mornig for you, when you read this, Now I have tryed the 
  flag in
the mri_mask command but it seems too similar to what was doing
before, it says that will transfer 1 voxel edits to dst vol, but 
  there
many more voxels edited, I have also tryed mri_vol2vol in the
brainmask.mgz intead of brain.mgz but the result is exactly the same
(the output from mri_vol2vol has the voxel 'deletions', but the
mri_mask ignore them. Now i have no idea how to solve this, do you?
   
Bests,
Gabriel
   
   
   
   
   
   
   
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Wed, 9 Mar 2011 18:00:37 -0500
   
we've improved some of the help text for the next version (5.1),
which
is the only reason i noticed it this time.
   
   
On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
   
Than you Nick,
   
Actually that was exactly what i did, delete some voxels from the
brainmask, I will try adding the flag and let you know, I dind't
saw
that this option exist in the mri_mask.
   
thank you again,
Gabriel
   
   
   
   
   
   
Subject: Re: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 9 Mar 2011 17:52:34 -0500
   
hi, not sure what you

Re: [Freesurfer] mri_mask problem

[Douglas N Greve]

For mri_vol2vol try using --interp nearest
doug

Gabriel Go.Es. wrote:

 Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or 
 brainmask2raw.gz to mask the rawavg.gz on the mri_mask. mri_mask -T 2 
 -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz
 And actually the brain.mgz and brainmask.mgz have values of one on 
 edited voxels, but after mri_vol2vol or mri_convert -rl the voxel 
 values appear with bigger values, and some of these values are like 
 ventricles values, so I can not just put a high threshold; new values  
 on edited voxels range from 1 to 40 approximately, and yes, the 
 background has values less than 2.
 Gabriel





  Date: Tue, 15 Mar 2011 13:30:40 -0400
  From: gr...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; 
 ni...@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] mri_mask problem
 
  Have you checked brainmask2raw.mgz? It looks like you've checked
  brain2raw.mgz, but you're not using it for some reason. Make sure the
  background has values less than 2.
  doug
 
  Gabriel Go.Es. wrote:
  
   Hello Bruce and Nick, I've tryed these options you said and still not
   works, I must say that is not in all my subjects,
  
   I've tryed both brain.mgz and brainmask.mgz.
  
   The commands I've used are:
  
   A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
   brain2raw.mgz --regheader
   A2) mri_mask flag -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz
   outbrain.mgz
  
   after mri_vol2vol the brain2raw.mgz look perfecty fine, but when
   apply the mri_mask the image apperars with no edits.
  
   B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz
   B2) mri_mask flag -T 2 -keep_mask_deletion_edits rawavg.mgz
   brainmask2raw.mgz outbrain2.mgz
  
   I've ran the mri_mask command with and without the
   -keep_mask_deletion_edits flag
   and again appears to be the mri_mask command the one that is not 
 doing
   the work, actually the outputs from mri_convert and mri_vol2vol, 
 looks
   pretty similar, any ideas?
  
   Bests
   Gabriel
  
  
  
  
  
Date: Mon, 14 Mar 2011 08:57:16 -0400
From: fis...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_mask problem
   
Hi Gabriel,
   
did you convert the brain.mgz so it is in the same space as the
rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you
   can try
mri_mask -t threshold. The default is 1e-10 so pretty much 
 anything
non-zero is dept. Try changing it to 2 (voxels edited to be turned
   off are
1).
   
cheers
Bruce
   
On Mon, 14 Mar 2011,
Gabriel Go.Es. wrote:
   

 Hello Nick

 I'm wondering if you're able to verify my data today,
 I did try using brainmask.mgz to mask the rawavg.mgz, and didn't
   worked,
 I'm guessing you'll need my data, to see if there is something
   wrong on it, but I think is gonna be hard to send it to through the
   e-mail.

 Bests,
 Gabriel.



 Subject: RE: [Freesurfer] mri_mask problem
 From: ni...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 Date: Thu, 10 Mar 2011 21:38:50 -0500

 i'd have to try to replicate this myself, although it will have
   to wait
 till monday (i'm with the freesurfer group three days a week).

 i wonder if you can use the brain.mgz as your mask instead of
 brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels 
 but
   their
 actually not there (zeroed).

 n.

 On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
 Hello Nick,
 good mornig for you, when you read this, Now I have tryed the
   flag in
 the mri_mask command but it seems too similar to what was doing
 before, it says that will transfer 1 voxel edits to dst vol, 
 but
   there
 many more voxels edited, I have also tryed mri_vol2vol in the
 brainmask.mgz intead of brain.mgz but the result is exactly 
 the same
 (the output from mri_vol2vol has the voxel 'deletions', but the
 mri_mask ignore them. Now i have no idea how to solve this, 
 do you?

 Bests,
 Gabriel







 Subject: RE: [Freesurfer] mri_mask problem
 From: ni...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 Date: Wed, 9 Mar 2011 18:00:37 -0500

 we've improved some of the help text for the next version 
 (5.1),
 which
 is the only reason i noticed it this time.


 On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:

 Than you Nick,

 Actually that was exactly what i did, delete some voxels 
 from the
 brainmask, I will try adding the flag and let you know, I 
 dind't
 saw
 that this option exist in the mri_mask.

 thank you again,
 Gabriel






 Subject: Re

Re: [Freesurfer] mri_mask problem

[Gabriel Go.Es.]

Hello Nick
 
I'm wondering if you're able to verify my data today, 
I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
I'm guessing you'll need my data, to see if there is something wrong on it, but 
I think is gonna be hard to send it to through the e-mail.

Bests,
Gabriel.


 
 Subject: RE: [Freesurfer] mri_mask problem
 From: ni...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 Date: Thu, 10 Mar 2011 21:38:50 -0500
 
 i'd have to try to replicate this myself, although it will have to wait
 till monday (i'm with the freesurfer group three days a week).
 
 i wonder if you can use the brain.mgz as your mask instead of
 brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
 actually not there (zeroed).
 
 n.
 
 On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
  Hello Nick,
  good mornig for you, when you read this, Now I have tryed the flag in
  the mri_mask command but it seems too similar to what was doing
  before, it says that will transfer 1 voxel edits to dst vol, but there
  many more voxels edited, I have also tryed mri_vol2vol in the
  brainmask.mgz intead of brain.mgz but the result is exactly the same
  (the output from mri_vol2vol has the voxel 'deletions', but the
  mri_mask ignore them. Now i have no idea how to solve this, do you?
  
  Bests,
  Gabriel
  
  
  
  
  
  
  
   Subject: RE: [Freesurfer] mri_mask problem
   From: ni...@nmr.mgh.harvard.edu
   To: gabriel...@hotmail.com
   Date: Wed, 9 Mar 2011 18:00:37 -0500
   
   we've improved some of the help text for the next version (5.1),
  which
   is the only reason i noticed it this time.
   
   
   On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:

Than you Nick,

Actually that was exactly what i did, delete some voxels from the
brainmask, I will try adding the flag and let you know, I dind't
  saw
that this option exist in the mri_mask.

thank you again,
Gabriel






 Subject: Re: [Freesurfer] mri_mask problem
 From: ni...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 CC: freesurfer@nmr.mgh.harvard.edu
 Date: Wed, 9 Mar 2011 17:52:34 -0500
 
 hi, not sure what you are trying to do, as the commands below
  seem
to do
 what i expect them to do, which is to create a masked
(skull-stripped)
 version of rawavg.mgz. what do you mean by 'manual segmentation
 changes'?, and what exactly is going wrong?
 
 if you deleted voxels in brainmask.mgz, then perhaps you need to
  add
the
 flag -keep_mask_deletion_edits to mri_mask to transfer those
  voxels
 ('deleted' voxels actually have a special value to indicate
deleted).
 
 n.
 
 
 
 On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
  
  Hello everybody,
  Sorry for the insistance, but I need to solve this...
  
  I'm making some manual segmentation changes in the
  brainmask.mgz
and
  using mri_vol2vol and mri_mask commands to apply these changes
  to
the
  rawavg.mgz, the output from the mri_vol2vol looks perfectly
normal,and
  retains all changed made by me, but when I use the mri_mask
command
  over the rawavg.mgz no segmentation seems to be donne in the
  final
  output file.
  
  
  Does any one has an idea of what could be wrong?
  
  
  the commands after manual corrections are:
  
  
  mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
  brain2raw.mgz
  --regheader
  mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
  
  
  
  
  Thanks in advanced,
  Gabriel
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
 The information in this e-mail is intended only for the person
  to
whom it is
 addressed. If you believe this e-mail was sent to you in error
  and
the e-mail
 contains patient information, please contact the Partners
  Compliance
HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent
  to
you in error
 but does not contain patient information, please contact the
  sender
and properly
 dispose of the e-mail.
 
   
 
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose

Re: [Freesurfer] mri_mask problem

[Bruce Fischl]

Hi Gabriel,

did you convert the brain.mgz so it is in the same space as the 
rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try 
mri_mask -t threshold. The default is 1e-10 so pretty much anything 
non-zero is dept. Try changing it to 2 (voxels edited to be turned off are 
1).

cheers
Bruce

On Mon, 14 Mar 2011, 
Gabriel Go.Es. wrote:


 Hello Nick

 I'm wondering if you're able to verify my data today,
 I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
 I'm guessing you'll need my data, to see if there is something wrong on it, 
 but I think is gonna be hard to send it to through the e-mail.

 Bests,
 Gabriel.



 Subject: RE: [Freesurfer] mri_mask problem
 From: ni...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 Date: Thu, 10 Mar 2011 21:38:50 -0500

 i'd have to try to replicate this myself, although it will have to wait
 till monday (i'm with the freesurfer group three days a week).

 i wonder if you can use the brain.mgz as your mask instead of
 brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
 actually not there (zeroed).

 n.

 On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
 Hello Nick,
 good mornig for you, when you read this, Now I have tryed the flag in
 the mri_mask command but it seems too similar to what was doing
 before, it says that will transfer 1 voxel edits to dst vol, but there
 many more voxels edited, I have also tryed mri_vol2vol in the
 brainmask.mgz intead of brain.mgz but the result is exactly the same
 (the output from mri_vol2vol has the voxel 'deletions', but the
 mri_mask ignore them. Now i have no idea how to solve this, do you?

 Bests,
 Gabriel







 Subject: RE: [Freesurfer] mri_mask problem
 From: ni...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 Date: Wed, 9 Mar 2011 18:00:37 -0500

 we've improved some of the help text for the next version (5.1),
 which
 is the only reason i noticed it this time.


 On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:

 Than you Nick,

 Actually that was exactly what i did, delete some voxels from the
 brainmask, I will try adding the flag and let you know, I dind't
 saw
 that this option exist in the mri_mask.

 thank you again,
 Gabriel






 Subject: Re: [Freesurfer] mri_mask problem
 From: ni...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 CC: freesurfer@nmr.mgh.harvard.edu
 Date: Wed, 9 Mar 2011 17:52:34 -0500

 hi, not sure what you are trying to do, as the commands below
 seem
 to do
 what i expect them to do, which is to create a masked
 (skull-stripped)
 version of rawavg.mgz. what do you mean by 'manual segmentation
 changes'?, and what exactly is going wrong?

 if you deleted voxels in brainmask.mgz, then perhaps you need to
 add
 the
 flag -keep_mask_deletion_edits to mri_mask to transfer those
 voxels
 ('deleted' voxels actually have a special value to indicate
 deleted).

 n.



 On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:

 Hello everybody,
 Sorry for the insistance, but I need to solve this...

 I'm making some manual segmentation changes in the
 brainmask.mgz
 and
 using mri_vol2vol and mri_mask commands to apply these changes
 to
 the
 rawavg.mgz, the output from the mri_vol2vol looks perfectly
 normal,and
 retains all changed made by me, but when I use the mri_mask
 command
 over the rawavg.mgz no segmentation seems to be donne in the
 final
 output file.


 Does any one has an idea of what could be wrong?


 the commands after manual corrections are:


 mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
 brain2raw.mgz
 --regheader
 mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz




 Thanks in advanced,
 Gabriel
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



 The information in this e-mail is intended only for the person
 to
 whom it is
 addressed. If you believe this e-mail was sent to you in error
 and
 the e-mail
 contains patient information, please contact the Partners
 Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent
 to
 you in error
 but does not contain patient information, please contact the
 sender
 and properly
 dispose of the e-mail.




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

Re: [Freesurfer] mri_mask problem

[Gabriel Go.Es.]

Helo Bruce, I've tryed these options you said and still not working, I must say 
that is not in all my subjects,
 
I've tryed both brain.mgz and brainmask.mgz.
 
The commands I've used are:

A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz 
--regheader
A2) mri_mask flag -keep_mask_deletion_edits  rawavg.mgz brain2raw.mgz 
outbrain.mgz
 
after mri_vol2vol the brain2raw.mgz look perfecty fine, but when apply the 
mri_mask the image apperars with no edits. 

B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz
B2) mri_mask flag -T 2 -keep_mask_deletion_edits  rawavg.mgz brainmask2raw.mgz 
outbrain2.mgz
 
I've ran the mri_mask command with and without the -keep_mask_deletion_edits 
flag
and again appears to be the mri_mask command the one that is not doing the 
work, actually the outputs from mri_convert and mri_vol2vol, looks pretty 
similar, any ideas?
 
Bests
Gabriel

 
 

 
 Date: Mon, 14 Mar 2011 08:57:16 -0400
 From: fis...@nmr.mgh.harvard.edu
 To: gabriel...@hotmail.com
 CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mri_mask problem
 
 Hi Gabriel,
 
 did you convert the brain.mgz so it is in the same space as the 
 rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try 
 mri_mask -t threshold. The default is 1e-10 so pretty much anything 
 non-zero is dept. Try changing it to 2 (voxels edited to be turned off are 
 1).
 
 cheers
 Bruce
 
 On Mon, 14 Mar 2011, 
 Gabriel Go.Es. wrote:
 
 
  Hello Nick
 
  I'm wondering if you're able to verify my data today,
  I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
  I'm guessing you'll need my data, to see if there is something wrong on it, 
  but I think is gonna be hard to send it to through the e-mail.
 
  Bests,
  Gabriel.
 
 
 
  Subject: RE: [Freesurfer] mri_mask problem
  From: ni...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  Date: Thu, 10 Mar 2011 21:38:50 -0500
 
  i'd have to try to replicate this myself, although it will have to wait
  till monday (i'm with the freesurfer group three days a week).
 
  i wonder if you can use the brain.mgz as your mask instead of
  brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
  actually not there (zeroed).
 
  n.
 
  On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
  Hello Nick,
  good mornig for you, when you read this, Now I have tryed the flag in
  the mri_mask command but it seems too similar to what was doing
  before, it says that will transfer 1 voxel edits to dst vol, but there
  many more voxels edited, I have also tryed mri_vol2vol in the
  brainmask.mgz intead of brain.mgz but the result is exactly the same
  (the output from mri_vol2vol has the voxel 'deletions', but the
  mri_mask ignore them. Now i have no idea how to solve this, do you?
 
  Bests,
  Gabriel
 
 
 
 
 
 
 
  Subject: RE: [Freesurfer] mri_mask problem
  From: ni...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  Date: Wed, 9 Mar 2011 18:00:37 -0500
 
  we've improved some of the help text for the next version (5.1),
  which
  is the only reason i noticed it this time.
 
 
  On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
 
  Than you Nick,
 
  Actually that was exactly what i did, delete some voxels from the
  brainmask, I will try adding the flag and let you know, I dind't
  saw
  that this option exist in the mri_mask.
 
  thank you again,
  Gabriel
 
 
 
 
 
 
  Subject: Re: [Freesurfer] mri_mask problem
  From: ni...@nmr.mgh.harvard.edu
  To: gabriel...@hotmail.com
  CC: freesurfer@nmr.mgh.harvard.edu
  Date: Wed, 9 Mar 2011 17:52:34 -0500
 
  hi, not sure what you are trying to do, as the commands below
  seem
  to do
  what i expect them to do, which is to create a masked
  (skull-stripped)
  version of rawavg.mgz. what do you mean by 'manual segmentation
  changes'?, and what exactly is going wrong?
 
  if you deleted voxels in brainmask.mgz, then perhaps you need to
  add
  the
  flag -keep_mask_deletion_edits to mri_mask to transfer those
  voxels
  ('deleted' voxels actually have a special value to indicate
  deleted).
 
  n.
 
 
 
  On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
 
  Hello everybody,
  Sorry for the insistance, but I need to solve this...
 
  I'm making some manual segmentation changes in the
  brainmask.mgz
  and
  using mri_vol2vol and mri_mask commands to apply these changes
  to
  the
  rawavg.mgz, the output from the mri_vol2vol looks perfectly
  normal,and
  retains all changed made by me, but when I use the mri_mask
  command
  over the rawavg.mgz no segmentation seems to be donne in the
  final
  output file.
 
 
  Does any one has an idea of what could be wrong?
 
 
  the commands after manual corrections are:
 
 
  mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
  brain2raw.mgz
  --regheader
  mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
 
 
 
 
  Thanks in advanced,
  Gabriel

[Freesurfer] mri_mask problem

[Gabriel Go.Es.]

 Hello,
I'm making some manual segmentation changes in the brainmask.mgz and using 
mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the 
output from the mri_vol2vol looks perfectly normal,and retains all changed made 
by me, but when I use the mri_mask command over the rawavg.mgz no segmentation 
seems to be donne in the final output file.
Does any one has an idea of what could be wrong?
the commands after manual corrections are:
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz 
--regheadermri_mask rawavg.mgz brain2raw.mgz outbrain.mgz

Thanks in advanced,Gabriel___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri_mask problem

[Gabriel Go.Es.]

 Hello everybody,Sorry for the insistance, but I need to solve this...

I'm making some manual segmentation changes in the brainmask.mgz and using 
mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the 
output from the mri_vol2vol looks perfectly normal,and retains all changed made 
by me, but when I use the mri_mask command over the rawavg.mgz no segmentation 
seems to be donne in the final output file.
Does any one has an idea of what could be wrong?
the commands after manual corrections are:
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz 
--regheadermri_mask rawavg.mgz brain2raw.mgz outbrain.mgz

Thanks in advanced,Gabriel___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_mask problem

[Nick Schmansky]

hi, not sure what you are trying to do, as the commands below seem to do
what i expect them to do, which is to create a masked (skull-stripped)
version of rawavg.mgz.  what do you mean by 'manual segmentation
changes'?, and what exactly is going wrong?

if you deleted voxels in brainmask.mgz, then perhaps you need to add the
flag -keep_mask_deletion_edits to mri_mask to transfer those voxels
('deleted' voxels actually have a special value to indicate deleted).

n.



On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
 
  Hello everybody,
 Sorry for the insistance, but I need to solve this...
 
 I'm making some manual segmentation changes in the brainmask.mgz and
 using mri_vol2vol and mri_mask commands to apply these changes to the
 rawavg.mgz, the output from the mri_vol2vol looks perfectly normal,and
 retains all changed made by me, but when I use the mri_mask command
 over the rawavg.mgz no segmentation seems to be donne in the final
 output file.
 
 
 Does any one has an idea of what could be wrong?
 
 
 the commands after manual corrections are:
 
 
 mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz
 --regheader
 mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
 
 
 
 
 Thanks in advanced,
 Gabriel
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[Freesurfer] mri_mask

[Gabriel Go.Es.]

Hello Freesurfers,
 
I'm trying to mask the rawavg.mgz from some subjects with  the brain.mgz after 
doing some manual segmentation corrections by using mri_mask command, I have 
donne it before and it always works but with this subject, the command line is 
excacly the same so I have no idea what could be wrong:
 
mri_mask rawavg.mgz brain.mgz outbrain.mgz 
 
ERROR: dimension mismatch between source and mask.

 Can any one help me with this?
 
Bests,
Gabriel

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Re: [Freesurfer] mri_mask

[Douglas Greve]

The rawavg.mgz and brain.mgz are of different sizes. You'll need to 
transfer one to the other. You can do this with mri_vol2vol using brain 
as the mov and rawavg as the target and --regheader.


doug

On 2/21/11 11:49 AM, Gabriel Go.Es. wrote:

Hello Freesurfers,

I'm trying to mask the rawavg.mgz from some subjects with  the 
brain.mgz after doing some manual segmentation corrections by using 
mri_mask command, I have donne it before and it always works but with 
this subject, the command line is excacly the same so I have no idea 
what could be wrong:


mri_mask rawavg.mgz brain.mgz outbrain.mgz

ERROR: dimension mismatch between source and mask.

 Can any one help me with this?

Bests,
Gabriel



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[Freesurfer] mri_mask

[Daniel H Choi]

Hi,

I have tried applying a binary mask, specifically for STG, in conjunction
with the mri_mask command. We applied it to a brainmask volume, but we did
not get the result we wanted. The output we recieved was simply the mask
that we used. We wish to produce an output that gives the STG volume alone
from the brain, and not from the binary mask. Are we using the command
incorrectly? Thanks

-- 
Daniel Horim Choi
Northwestern University
Class of 2009
[EMAIL PROTECTED] or
[EMAIL PROTECTED]
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[Freesurfer] mri_mask bug

[Yuhong Jiang]

Hi,

We were running free-surfer (freesurfer-Linux-rh9-dev20051003-full.tar.gz) 
on RedHat 9 and encountered a problem with the command mri_mask. It is not 
at all working.


Here is what we entered as input:
mri_mask input.mgz mask.mgz output.mgz

No matter what we put as the mask, the input.mgz and output.mgz are always 
identical. Is there a bug with this command?
(The command says  writing masked volume to output.mgz... then about 10 
seconds later it's done - although nothing is done).


Thanks.

--Yuhong
=
Yuhong Jiang[EMAIL PROTECTED]
617-876-2054http://web.mit.edu/yuhong/www
=
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Re: [Freesurfer] mri_mask bug

[Bruce Fischl]

what is in the mask.mgz volume?

On Fri, 6 Jan 2006, Yuhong Jiang wrote:


Hi,

We were running free-surfer (freesurfer-Linux-rh9-dev20051003-full.tar.gz) on 
RedHat 9 and encountered a problem with the command mri_mask. It is not at 
all working.


Here is what we entered as input:
mri_mask input.mgz mask.mgz output.mgz

No matter what we put as the mask, the input.mgz and output.mgz are always 
identical. Is there a bug with this command?
(The command says  writing masked volume to output.mgz... then about 10 
seconds later it's done - although nothing is done).


Thanks.

--Yuhong
=
Yuhong Jiang[EMAIL PROTECTED]
617-876-2054http://web.mit.edu/yuhong/www
=
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