Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

Re: [Freesurfer] ICV/brain volume
by Bruce Fischl 11 Jan '10

11 Jan '10

Hi Xiangchuan, the cerebral gray matter volume should be the difference between the mris_volume of the pial and white surfaces. cheers Bruce On Sat, 9 Jan 2010, 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:mreuter@nmr.mgh.harvard.edu] >> Sent: Saturday, January 09, 2010 13:34 >> To: Bruce Fischl >> Cc: Michael Harms; Xiangchuan Chen; freesurfer(a)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 <fischl(a)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:mharms@conte.wustl.edu] >>>>> Sent: Friday, January 08, 2010 15:55 >>>>> To: Xiangchuan Chen >>>>> Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> > > >

2 1

only color premotor gyrus use annotation file
by tulu 11 Jan '10

11 Jan '10

Dear Freesurfer experts, I wish to draw a selected gyrus on the whole hemisphere. Could I only color display the selected gyrus and use other color on all others gyrus from annotation file ? if yes, how to do it. Thank help Kl chen

2 1

Keyboard input error
by SG KIM 11 Jan '10

11 Jan '10

Dear all, I just started TKSURFER (v4.5.0) on Ubuntu 9.10 (karmic koala/i386). Before I get hands real dirty, I found that I cannot type anything in text field of Freesurfer's GUI: I can't even type a 'basename' saving multiple views. :( I'm a newbie for Linux. Anybody have a suggestion?

1 0

Re: [Freesurfer] ICV/brain volume
by Martin Reuter 10 Jan '10

10 Jan '10

Yes, there are several Talairach transforms with different purposes. The troubleshoot workflow really needs to be updated. Using T2 should really help getting better icv measures. We will be playing around with multimodal processing. Hopefully this will lead also to better ivc. Best Martin On Jan 10, 2010, at 0:55, "Xiangchuan Chen" <xiangchuan.chen(a)bme.emory.edu > wrote: > 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:mreuter@nmr.mgh.harvard.edu] >> Sent: Saturday, January 09, 2010 22:05 >> To: Xiangchuan Chen; Nick Schmansky >> Cc: 'Bruce Fischl'; 'Michael Harms'; freesurfer(a)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:mreuter@nmr.mgh.harvard.edu] >>>> Sent: Saturday, January 09, 2010 13:34 >>>> To: Bruce Fischl >>>> Cc: Michael Harms; Xiangchuan Chen; freesurfer(a)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 <fischl(a)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:mharms@conte.wustl.edu] >>>>>>> Sent: Friday, January 08, 2010 15:55 >>>>>>> To: Xiangchuan Chen >>>>>>> Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>> >>> > >

1 0

Re: [Freesurfer] ICV/brain volume
by Martin Reuter 10 Jan '10

10 Jan '10

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:mreuter@nmr.mgh.harvard.edu] > > Sent: Saturday, January 09, 2010 13:34 > > To: Bruce Fischl > > Cc: Michael Harms; Xiangchuan Chen; freesurfer(a)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 <fischl(a)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:mharms@conte.wustl.edu] > > >>> Sent: Friday, January 08, 2010 15:55 > > >>> To: Xiangchuan Chen > > >>> Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu > > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer(a)nmr.mgh.harvard.edu > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > >> > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > >

2 1

Re: [Freesurfer] ICV/brain volume
by Michael Harms 09 Jan '10

09 Jan '10

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 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:mreuter@nmr.mgh.harvard.edu] >> Sent: Saturday, January 09, 2010 13:34 >> To: Bruce Fischl >> Cc: Michael Harms; Xiangchuan Chen; freesurfer(a)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 <fischl(a)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:mharms@conte.wustl.edu] >> >>> Sent: Friday, January 08, 2010 15:55 >> >>> To: Xiangchuan Chen >> >>> Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu >> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >

1 0

Re: [Freesurfer] ICV/brain volume
by Michael Harms 09 Jan '10

09 Jan '10

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:mharms@conte.wustl.edu] > Sent: Friday, January 08, 2010 15:55 > To: Xiangchuan Chen > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

4 3

Re: [Freesurfer] ICV/brain volume
by Michael Harms 08 Jan '10

08 Jan '10

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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Smoothing BOLD on the surface
by Oya, Hiroyuki 08 Jan '10

08 Jan '10

Dear Experts, I would like to first analyze the BOLD response without smoothing in the functional volume, and apply smoothing on the surface and map it. Would this be possible? Thank you in advance. Hiroyuki

2 1

Order of structures in aparcstats2table
by Dankner, Nathan (NIH/NIMH) [F] 08 Jan '10

08 Jan '10

Hi All, I just started using version 4.5, and when I use aparcstats2table to create a table the structures are being listed in a strange order. The ?h.aparc.stats file itself has them in the order in which they were in previous versions (essentially alphabetical except for frontal pole), but for whatever reason when made into a .txt file with aparcs2statstable it seems to jumble them up (but in a consistent way). Any ideas regarding how to get the program to order them in the older standard way?

2 2

← Newer
1
...
7
8
9
10
11
12
13
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer January 2010