Hi Martin,
I usually follow the "FreeSurfer Troubleshooting Reconstruction Work Flow"
to do recon-all. So, I run "tkregister2 --mgz --s your_subject_name --fstal"
to edit talairach transform. On ~/ fswiki/eTIV it is suggested to run "
tkregister2 --xfm talairach.xfm --targ
$FREESURFER_HOME/average
Hi Xiangchuan,
In recent versions of Freesurfer, the atlas
$FREESURFER_HOME/average/711-2C_as_mni_average_305.4dfp.img and the
registration to that atlas found in
$SUBJECTS_DIR/subjid/mri/transforms/talairach.xfm (created by
talairach_avi, a script which calls imgreg_4dfp) is used to estimate ICV
If you want to establish that the changes in a given region are in excess
of any global atropy, then yes, I would agree that you want to use a
measure of brain volume rather than ICV as a covariate.
-MH
> Hi Martin, Bruce and Mike,
>
> Thank you for all your suggestions.
>
> For Martin's suggest
Hi Martin, Bruce and Mike,
Thank you for all your suggestions.
For Martin's suggestion: I found that it is hard to really fix the talairach
transform for a lot of my subjects. In most cases, I tried to match the
outlines between target and moveable images when running "tkregister2 --mgz
--fstal -
Or you can fix the talairach transform and get the icv the standart way.
When dividing by total brain vol, you undo atrophy. That's why icv is
used.
Martin
On Jan 9, 2010, at 13:01, Bruce Fischl
wrote:
> or you could use mris_wm_volume, which excludes the interior of the
> ventricles and g
or you could use mris_wm_volume, which excludes the interior of the
ventricles and gray matter structures, and mris_volume and the aseg to
calculate it (adding the structures you are interested back in). Maybe we
should start generating this # by default. Would enough people find it
useful?
ch
You're correct that a small amount of hippocampus and amygdala falls
outside the pial surface. However, it will be a TINY percentage of the
whole brain volume, and MUCH smaller than variation of brain volume across
individuals. So the little bit of hippocampus and amygdala that is
"missed" will
