Hi Anil,
in tkmedit you mean? Sure, you can change contrast and brightness to
match the whole volume (and min and max).
cheers,
Bruce
On Sun, 11 May 2008, Anil Roy
wrote:
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 <[EMAIL PROTECTED]>
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
[EMAIL PROTECTED] 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 <
[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]>
Date: Fri, May 9, 2008 at 8:21 PM
Subject: Re: [Freesurfer] Re: mri_mask
To: Daniel H Choi <[EMAIL PROTECTED]>
Cc: Krish Subramaniam <[EMAIL PROTECTED]>
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 <
[EMAIL PROTECTED]>
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
[EMAIL PROTECTED] or
[EMAIL PROTECTED]
--
Daniel Horim Choi
Northwestern University
Class of 2009
[EMAIL PROTECTED] or
[EMAIL PROTECTED]
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