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