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

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

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

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 wrote:External Email - Use CautionHello,FYI, I recently noticed that

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

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 ou

[Freesurfer] mri_mask error exits returns a zero exit status

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 https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] Mri_mask producing only zeros

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 > out

Re: [Freesurfer] Mri_mask producing only zeros

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 int

Re: [Freesurfer] Mri_mask producing only zeros

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.

Re: [Freesurfer] Mri_mask producing only zeros

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

[Freesurfer] Mri_mask producing only zeros

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 labe

Re: [Freesurfer] mri_mask output problem

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

Re: [Freesurfer] mri_mask output problem

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 t

Re: [Freesurfer] mri_mask output problem

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 th

Re: [Freesurfer] mri_mask output problem

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_m

Re: [Freesurfer] mri_mask output problem

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

Re: [Freesurfer] mri_mask output problem

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 conta

[Freesurfer] mri_mask output problem

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

Re: [Freesurfer] mri_mask problem

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_mas

Re: [Freesurfer] mri_mask problem

om > > 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 reas

Re: [Freesurfer] mri_mask problem

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 checke

Re: [Freesurfer] mri_mask problem

rt 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@n

Re: [Freesurfer] mri_mask problem

ol2vol, 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 >

Re: [Freesurfer] mri_mask problem

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, >

Re: [Freesurfer] mri_mask problem

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

Re: [Freesurfer] mri_mask problem

e 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 mond

Re: [Freesurfer] mri_mask problem

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

[Freesurfer] mri_mask problem

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 c

[Freesurfer] mri_mask problem

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 th

Re: [Freesurfer] mri_mask

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.mg

[Freesurfer] mri_mask

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

[Freesurfer] mri_mask

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 alo

Re: [Freesurfer] mri_mask bug

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

[Freesurfer] mri_mask bug

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