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:
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
Hello,
FYI, I recently noticed that mri_mask returns a zero exit status when it is
unable to write the output.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
>
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
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
: [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
.
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
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
?
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
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
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
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
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
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
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
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
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
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