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.
