Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Douglas N Greve
el to ras transform: >>-0.0553 0.0101 -0.9984 129.8205 >> 0.9863 0.1563 -0.0530 -127.5422 >> 0.1555 -0.9877 -0.018699.3136 >> 0.0000 0. 0. 1. >> >> voxel-to-ras det

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Bruce Fischl
0 1. > > Best, > Idil > ____________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 > [yozdemi...@amherst.edu] > Sent: Thursday, August 17, 2017 7:07 PM > To: Freesurfer s

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Yagmur Ozdemir 19
urfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, August 17, 2017 7:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem/mri_mask Hi Idil you need to give us much

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Yagmur Ozdemir 19
-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, August 17, 2017 7:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem/mri_mask Hi Idil you need to give us much more informati

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Bruce Fischl
__ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, August 17, 2017 6:55 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mask alignment prob

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Bruce Fischl
gh.harvard.edu] > Sent: Thursday, August 17, 2017 6:50 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mask alignment problem/mri_mask > > sorry, I don't understand > Bruce > On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote: > >> Thank you! >> >> T

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Yagmur Ozdemir 19
...@nmr.mgh.harvard.edu] Sent: Thursday, August 17, 2017 6:50 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem/mri_mask sorry, I don't understand Bruce On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote: > Thank you! > > Then I guess I would use the volume as the transform file

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Bruce Fischl
gh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, August 17, 2017 6:41 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mask alignment problem/mri_mask > > ok, but your mri_mask comm

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Yagmur Ozdemir 19
: Thursday, August 17, 2017 6:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem/mri_mask ok, but your mri_mask command line has the string "%s" in it, which is not correct. You need to specify an actual file name. I also think you are better off using mri_c

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Bruce Fischl
> From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, August 17, 2017 6:14 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mask alignment problem/mri_mas

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Yagmur Ozdemir 19
[fis...@nmr.mgh.harvard.edu] Sent: Thursday, August 17, 2017 6:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem/mri_mask Hi Idil how did you create the mask and the transform? Also, you can't specify "%s" on the command line - you need an actual name of a transform

Re: [Freesurfer] mask alignment problem/mri_mask

2017-08-17 Thread Bruce Fischl
Hi Idil how did you create the mask and the transform? Also, you can't specify "%s" on the command line - you need an actual name of a transform file. cheers Bruce On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote: Hello freesurfer experts, A volume file I want to save as a mask(the orange