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/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk " to check the quality of talairach.xfm. I guess I should follow the method on the eTIV wiki to fix talairach transform, and the "Work Flow" wiki might need to be revised?
For ICV: I also think that for normally developed, and then impaired or degenerated brains, ICV is a good index for normalization purpose. For brains with development problems, total brain volume may be a better index than ICV. In either case, we need accurate value for these indices. I remember that several previous posts mentioned that ICV could be "measured" based on T2 images. Hope that this feature will be implemented in FreeSurfer. Thanks, Xiangchuan > -----Original Message----- > From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] > Sent: Saturday, January 09, 2010 22:05 > To: Xiangchuan Chen; Nick Schmansky > Cc: 'Bruce Fischl'; 'Michael Harms'; freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] ICV/brain volume > > 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 > (the '711-2C' atlas target image includes skull). > > So only talairach.xfm needs to be accurate for ICV to be good. You need > to check it with the corresponding atlas (maybe Nick can verify that > this is correct). > Here http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV is some background. > > Also: > "ICV (sum of effects, but is estimated)". No, ICV should not show any > effects (total intracranial volume should not change with atrophy). > That > is why it is usually used for normalizing. But Micheal is right, if you > want to show 'extra' effect of specific regions, you're probably fine. > > Cheers, Martin > > On Sat, 2010-01-09 at 20:08 -0500, Xiangchuan Chen wrote: > > 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 --s subjid" (step1). For some of these subjects, I also > checked the > > talairach transform by running "tkregister2 --xfm talairach.xfm -- > targ > > $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov > > ../nu_noneck.mgz --reg junk" (step2), and found that the moveable and > target > > images were not aligned very well (looked worse than in step1). In > this > > case, do I need to further edit the talairach transform in step2? > > > > The reason for adjusting with total brain volume: In our study, we > found > > difference in ICV and a lot of cortical and sub-cortical regions > between > > groups. Then, we want to know if some of these regions showed extra > effect > > than other regions. For this purpose, using total brain volume (sum > of > > effects on these regions) may be better than using ICV (sum of > effects, but > > is estimated). Please correct me if I am wrong here. > > > > For Bruce's suggestion: the cerebral white matter volume (calculated > with > > mris_wm_volume) is already in aseg.stats. Is there a way to calculate > the > > cerebral gray matter volume (surface based, more accurate)? I assume > that I > > can use the sum of the volumes from aparc.stats. > > > > Thanks, > > Xiangchuan > > > > > > > -----Original Message----- > > > From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] > > > Sent: Saturday, January 09, 2010 13:34 > > > To: Bruce Fischl > > > Cc: Michael Harms; Xiangchuan Chen; freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] ICV/brain volume > > > > > > 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 <fis...@nmr.mgh.harvard.edu> > > > wrote: > > > > > > > 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? > > > > > > > > cheers, > > > > Bruce > > > > > > > > On Sat, > > > > 9 Jan 2010, Michael Harms wrote: > > > > > > > >> > > > >> 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 be inconsequential in my opinion. > > > >> > > > >> cheers, > > > >> Mike H. > > > >> > > > >>> Hi Mike, > > > >>> > > > >>> Thanks for your suggestions. I have learned this idea from > > > >>> previous posts > > > >>> (including yours), but found that there is an issue for this > > > >>> approach when > > > >>> I > > > >>> checked the pial surface with tkmedit (tkmedit subjid T1.mgz > > > lh.pial > > > >>> -aux-surface rh.pial): part of two important brain structures, > > > >>> amygdala > > > >>> and > > > >>> hippocampus, is not enclosed in the pial surface. Is there a > way to > > > >>> resolve > > > >>> this issue? > > > >>> > > > >>> Thanks, > > > >>> Xiangchuan > > > >>> > > > >>> -----Original Message----- > > > >>> From: Michael Harms [mailto:mha...@conte.wustl.edu] > > > >>> Sent: Friday, January 08, 2010 15:55 > > > >>> To: Xiangchuan Chen > > > >>> Cc: freesurfer@nmr.mgh.harvard.edu > > > >>> Subject: Re: [Freesurfer] ICV/brain volume > > > >>> > > > >>> > > > >>> Here is an approach that will be easier, and involves less back > and > > > >>> forth between the surface and volume-based streams (and thus > > > >>> should be > > > >>> more accurate): Just use 'mris_volume' to get the volume of > > > >>> everything > > > >>> enclosed by the pial surface, which if I recall correctly will > > > >>> include > > > >>> the lateral ventricles, choroid plexus, and usually most of the > > > >>> inferior > > > >>> lateral ventricles (but not the 3rd and 4th ventricles). Then, > if > > > >>> you > > > >>> want to exclude ventricles from your definition of "brain > volume", > > > >>> just > > > >>> subtract the Lateral-Ventricle, choroid-plexus, and Inf-Lat- > Vent > > > >>> volumes > > > >>> (taken from the aseg.stats). > > > >>> > > > >>> cheers, > > > >>> Mike H. > > > >>> > > > >>> > > > >>> On Fri, 2010-01-08 at 15:13 -0500, Xiangchuan Chen wrote: > > > >>>> Dear FreeSurfer experts, > > > >>>> > > > >>>> After searching on FreeSurfer wiki and mailing list, I know > that > > > >>>> the ICV > > > >>>> reported in aseg.stats is an estimated value based on > talairach > > > >>>> transformation. So, if the talairach transformation for a > > > >>>> subject's head > > > >>> is > > > >>>> not good, the ICV for this subject is not accurate, am I right? > > > >>>> > > > >>>> If this is the case, it may not be suitable to use ICV to > adjust > > > >>>> the > > > >>>> volumetric data in aseg.stats and ?h.aparc.stats for some > special > > > >>> subjects. > > > >>>> I am thinking of using "brain volume" for this purpose. Here > are > > > >>>> the > > > >>>> steps > > > >>>> to get it: > > > >>>> > > > >>>> 1. Get the surface-based volume of cerebral white matter > > > >>>> (aseg.stats). > > > >>>> > > > >>>> 2. Add up the volumes of all cortical regions to get the > surface- > > > >>>> based > > > >>>> volume of cerebral cortex (aparc.stats). > > > >>>> > > > >>>> 3. Add up the above volumes (including both hemispheres) and > the > > > >>>> volumes > > > >>> of > > > >>>> all other regions listed in aseg.stats (except for cerebral > white > > > >>>> matter > > > >>> and > > > >>>> cerebral cortex) to get the brain volume. > > > >>>> > > > >>>> Is this a suitable way to obtain more accurate brain volume? > > > >>>> > > > >>>> Thanks in advance and any suggestions are greatly appreciated, > > > >>>> > > > >>>> Xiangchuan Chen > > > >>>> > > > >>>> > > > >>>> _______________________________________________ > > > >>>> 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 > > > >> > > > >> > > > >> > > > > _______________________________________________ > > > > 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
