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

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 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