At some point in early 2008, Doug had created a version of tkregister2
that he graciously provided us, which had --gca-skull and --gca flags,
which greatly simplified the process of confirming the accuracy of
either the talairach_with_skull.lta and talairach.lta transforms
(respectively). However, neither of those flags are options in the
current public release of FS 4.0.5.
Doug: Will the forthcoming FS release have those flags available as
options to tkregister2? We've found them to be a very helpful addition
to tkregister2, and it sounds like Jeff would as well.
Jeff: In the interim, here are my notes on how to do what you want to
accomplish (N.B. Doug's improved tkregister2 using the --gca-skull flag
is a more powerful approach because it makes the target the subject
space and thus the surfaces can also be meaningfully displayed via the
--surf option):
mri_convert $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca
RB_gca.mgz --frame 0
(N.B. add --conform option if you want to avoid format conversion within
tkregister2 itself (which slows loading))
tkregister2 --targ RB_gca.mgz --mov nu_noneck.mgz \
--lta transforms/talairach_with_skull.lta --reg tmp.reg
cheers,
-Mike H.
On Mon, 2008-09-08 at 15:54 -0600, Jeff Sadino wrote:
Hello,
I am trying to validate the ICV value by lining up the nu_noneck image with the RB image. These are the commands I am using:
mri_convert nu_noneck.mgz --apply_transform transforms/talairach_with_skull.lta nu_noneck5.mgz
tkmedit -f nu_noneck5.mgz &
tkmedit -f /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca &
When I compare these two, they don't line up. The RB image is all blurry (Maybe it's a combination of several subjects and is supposed to be like that). Any suggestions as to how to line up the noneck transformed imaged to the RB image is greatly appreciated!
I also attached three files to show what's happening in my transform process.
Thanks,
Jeff
----------------------------------------
Date: Fri, 5 Sep 2008 20:31:55 -0400
From: fischl@nmr.mgh.harvard.edu
To: jsadino@hotmail.com
Subject: RE: [Freesurfer] Talairach_with_skull.lta accuracy
can you send this to the list so others can respond? Where did you get the
tmp.reg file? If you have transformed them already you shouldn't need
tkregister2 (or a registration file in general) to compare them.
On Fri, 5 Sep 2008,
Jeff Sadino wrote:
Thank you very much for your help. Your knowledge and quick responses are very much appreciated.
I converted my image into transformed space, but it still does not match the RB image. These are the commands I used:
mri_convert nu_noneck.mgz --apply_transform
transforms/talairach_with_skull.lta nu_noneckt3.mgz
tkregister2 --targ
/apps/freesurfer/average/RB_all_withskull_2006-02-15.gca --reg tmp.reg
--lta /data/040002_S04_bakj/mri/transforms/talairach_with_skull.lta --mov
/data/040002_S04_bakj/mri/nu_noneckt3.mgz
Again, my main goal is to verify the ICV value, so to do that I need to verify that the lta file is transforming the nu_noneck image onto the RB image...I think.
What step am I missing?
Thank you
Jeff
----------------------------------------
Date: Fri, 5 Sep 2008 13:09:21 -0400
From: fischl@nmr.mgh.harvard.edu
To: jsadino@hotmail.com
CC: greve@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Talairach_with_skull.lta accuracy
that won't generate a transformed volume, just display it in the
transformed space. That is, the volumes you sent were in their native
space and would have no reason to be aligned. The neck removal seems to
have been fine in both cases.
On Thu, 4 Sep 2008, Jeff Sadino wrote:
ps, sorry, I forgot to include my command:
tkregister2 --targ /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca --mov /data/${file}/mri/nu_noneck.mgz --lta /data/${file}/mri/transforms/talairach_with_skull.lta --reg tmp.reg
I believe this will transform the nu_neck.mgz image via the talairach matrix, so that it matches the RB image.
btw, we processed the scans using freesurfer 3, but the tkregister2 that came with freesurfer 3 did not include the --lta tag, so I am using the tkregister2 from freesurfer4.
Thanks!
----------------------------------------
Date: Thu, 4 Sep 2008 21:49:27 -0400
From: fischl@nmr.mgh.harvard.edu
To: jsadino@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach_with_skull.lta accuracy
Hi Jeff,
why do you say that one is bad? We don't resample, so neither one will be
aligned with the atlas unless you apply the transform.
We are aware that the eTIV measures have more variability than we would
like, and we're looking into it, but don't have a good solution from only
T1 images.
cheers,
Bruce
On Thu, 4 Sep 2008,
Jeff Sadino wrote:
Hello all,
According to aseg.stats, our ICV values fluctuate on the same subject across scans, sometimes by up to 10% I have been validating the talairach_with_skull.lta accuracy by comparing the nu_neck.mgz to the RB_all_withskull_2006-02-15.gca template. I read on the boards that it is not all that necessary that the brains match, that it is more important for the skulls to match. The RB is blurred (I don't fully understand where the RB comes from, I think from 22 subjects that the freesurfers combined into one?), so am I matching up the whitest areas of the RB to the skull on the nu_neck image? I noticed also that the bottom of the brains rarely match at all to the RB image...is this normal? Are there any other parts of the image that need to be checked for validity?
I attached two nu_noneck.mgz files, one was good and the other bad. Are these images typical?
Thank you for your help,
Jeff
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