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: [EMAIL PROTECTED]
> > To: [EMAIL PROTECTED]
> > 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: [EMAIL PROTECTED]
> >>> To: [EMAIL PROTECTED]
> >>> CC: [EMAIL PROTECTED]
> >>> 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: [EMAIL PROTECTED]
> >>>>> To: [EMAIL PROTECTED]
> >>>>> 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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