Hi Bruce,

I'm working with Dan on this.

Yes, it does seem to work - sorry for the confusion. I was looking at the output without zooming in and it seemed to have only one intensity inside the mask, but on zooming in I could see the variations in intensity.

I did have an additional question - is it possible to increase the gray versus white matter contrast for the output. It seems that the brainmask volume has a lot more contrast than the output.

Thanks for your help,

Anil.

On Sat, May 10, 2008 at 8:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Dan,

this seems to work for me. I ran:

mri_mask brainmask.mgz lh.stg.mask.mgz test.mgz

and test had the intensity values from brainmask.mgz inside the non-zero region of lh.std.mask.mgz and 0 everywhere else. I've attached the results. Is this not what you get?

cheers
Bruce


On Sat, 10 May 2008, Daniel H Choi wrote:

Hi Bruce,

The following is the output that my colleague was able to render after
running the mri_mask again. Also attached are the brainmask.mgz and
lh.stg.mask.mgz files too. Would you be able to point out what went wrong?
Thanks.

Dan

[root@slr08 masks]# mri_info lh.stg.mask.mgz
Volume information for lh.stg.mask.mgz
        type: MGH
  dimensions: 256 x 256 x 256
 voxel sizes: 1.0000, 1.0000, 1.0000
        type: INT (1)
         fov: 256.000
         dof: 0
      xstart: -128.0, xend: 128.0
      ystart: -128.0, yend: 128.0
      zstart: -128.0, zend: 128.0
          TR: 2300.00 msec, TE: 3.36 msec, TI: 900.00 msec, flip angle:
9.00 degrees
     nframes: 1
ras xform present
  xform info: x_r =  -1.0000, y_r =  -0.0000, z_r =  -0.0000, c_r =
-0.4948
            : x_a =  -0.0000, y_a =  -0.0000, z_a =   1.0000, c_a =
47.1750
            : x_s =  -0.0000, y_s =  -1.0000, z_s =  -0.0000, c_s =
19.0414

talairach xfm :
/mnt/win/MRI_data/Trial_Runs/Freesurfer/E-08/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
             -1.0000  -0.0000  -0.0000   127.5052
             -0.0000  -0.0000   1.0000   -80.8250
             -0.0000  -1.0000  -0.0000   147.0414
              0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
             -1.0000  -0.0000   0.0000   127.5052
              0.0000   0.0000  -1.0000   147.0414
             -0.0000   1.0000   0.0000    80.8250
              0.0000   0.0000   0.0000     1.0000


Anil.


On Sat, May 10, 2008 at 1:50 PM, Daniel H Choi <dhchoi@u.northwestern.edu>
wrote:

Hey Anil,

This is what Bruce sent me just in case you needed verbatim what he said.
Thanks. And i'll forward him your results as soon as I get them from you.
Laters

Dan

---------- Forwarded message ----------
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Date: Fri, May 9, 2008 at 8:21 PM
Subject: Re: [Freesurfer] Re: mri_mask
To: Daniel H Choi <dhchoi@u.northwestern.edu>
Cc: Krish Subramaniam <krish@nmr.mgh.harvard.edu>


Hi Daniel,

I just tested this on some data and it seemed to work for me. Can you run
mri_info on the lh.STG.mgz volume and send us the results? And maybe you can
email me and Krish (ccd) the 2 volumes (brainmask.mgz and lh.STG.mgz) so we
can see if we can replicate it.

cheers,
Bruce

 On Fri, 9 May 2008, Daniel H Choi wrote:

 Please note the command we used:

mri_mask brainmask.mgz lh.stg.mask.mgz brainout.mgz

and the result we got was:

Writing masked volume to brainout.mgz...done.

On Fri, May 9, 2008 at 2:39 PM, Daniel H Choi <dhchoi@u.northwestern.edu>
wrote:

 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
dhchoi@u.northwestern.edu or
dchoi1024@gmail.com









--
Daniel Horim Choi
Northwestern University
Class of 2009
dhchoi@u.northwestern.edu or
dchoi1024@gmail.com






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