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