As I said, there are several talairach transforms. You need to look at the talairach.xfm.
The wiki says: To check the quality of the registration file talairach.xfm file: cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk Martin On Tue, 2010-12-21 at 20:12 +0100, Diederick Stoffers wrote: > Hi Martin, > > > I read the wiki on eTIV after finding this outlier. I used > > > tkregister2 --mgz --s subject --fstal --surf orig > > > to check the registration, that looked pretty decent. Any other > pointers? > > > Thanks! > > > Diederick > > > > On 21 dec 2010, at 17:40, Martin Reuter wrote: > > > Hi Diederick, > > > > the ICV is computed from the linear talairach.xfm transform > > (including > > skull). There are all kinds of other talairach transforms produced > > by > > recon all, so make sure you are looking at the talairach.xfm > > (not ...lta > > or ..._with_skull.lta). > > > > You might want to read: > > http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV > > > > It is very likely that the clipping on your outlier image (missing > > cerebellum etc). produce an incorrect talairach.xfm and thus outlier > > ICV. > > > > Best, Martin > > > > On Tue, 2010-12-21 at 17:32 +0100, Diederick Stoffers wrote: > > > Hi Martin, > > > > > > > > > OK, I didn't expect different scanners/fieldstrengths to have that > > > big > > > an effect on ICV. Given that there is a systematic bias, one would > > > expect a very high correlation between ICV at timepoint one and > > > two. I > > > inspected a scatterplot and this was indeed the case, except for a > > > single outlier. The Tailairach registration looks fine for both > > > timepoints in this outlier. However, the scan at one timepoint > > > was > > > badly planned, part of the cerebellum and brainstem are missing. > > > Could > > > this explain the low ICV value in this subject? If not, what other > > > things should I check? > > > > > > > > > Cheers, > > > > > > > > > Diederick > > > > > > On 20 dec 2010, at 15:26, Martin Reuter wrote: > > > > > > > Hi Diederick, > > > > > > > > In a longitudinal study you need to ensure identical acquisition > > > > and > > > > processing, else you'll introduce a systematic bias. > > > > Some of my recent analyses indicate that even updating the > > > > software > > > > on the scanner can bias your results. Hardware changes are > > > > worse. > > > > > > > > Best Martin > > > > > > > > On Dec 20, 2010, at 6:48 AM, Diederick Stoffers > > > > <d.stoff...@gmail.com> wrote: > > > > > > > > > Hi all, > > > > > > > > > > I have a dataset with AD patients that were scanned twice, > > > > > once at > > > > > 1.5T and once at 3T at an interval of a few years. The ICV > > > > > values > > > > > are lower for almost all subjects at timepoint two (FS 5.0). > > > > > Isn't > > > > > ICV in the later FS versions supposed to be independent of > > > > > brain > > > > > volume as it is based on a scaling factor derived from the > > > > > Tailairach transform of the skull? Many thanks! > > > > > > > > > > Cheers, > > > > > > > > > > Diederick > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
