Re: [Freesurfer] ICV normalization (longitudinal pipeline)

Hi Martin, ICV is head size. It is unlikely that anything except head growth in children changes head size. I don’t know of drugs that do that ;-). So it is best to assume that head size is fixed for adults. Usually results should have less variance if you remove the noise from the ICV estimat

[Freesurfer] ICV normalization (longitudinal pipeline)

External Email - Use Caution Hello FS experts, I am using longitudinal processing pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) to calculate the cortical volume (CV) over a course of treatment (two conditions: pre condition and post condition). In fa

[Freesurfer] ICV bias in CV measures

External Email - Use Caution Dear FS experts, This paper was published in 2013: https://www.sciencedirect.com/science/article/pii/S1053811913007064?via%3Dihub#s0040 I was just wondering if the current version of FreeSurfer can still introduce bias in cortical volume measures if I

Re: [Freesurfer] ICV as covariate for controls vs. patients

External Email - Use Caution Thanks a lot Dr. Greve, that really helps. On Thu, Jul 26, 2018 at 10:45 AM, Douglas Greve wrote: > They give different results because they are supposed to. It may be that > the effect you are seeing without regressing out ICV is due to ICV, and > w

Re: [Freesurfer] ICV as covariate for controls vs. patients

They give different results because they are supposed to. It may be that the effect you are seeing without regressing out ICV is due to ICV, and when you control for ICV the effect goes away. It could also be that the ICV causes the variance to increase. This is why I asked you to check the rst

Re: [Freesurfer] ICV as covariate for controls vs. patients

If you are using surface area or volume, then you need ICV On 7/25/18 1:51 PM, Martin Juneja wrote: External Email - Use Caution Dr. Greve, I am sorry if my questions were not clear in previous email. Basically, I do not know what to conclude from this gamma comparison i.e. with and

Re: [Freesurfer] ICV as covariate for controls vs. patients

External Email - Use Caution Dr. Greve, I am sorry if my questions were not clear in previous email. Basically, I do not know what to conclude from this gamma comparison i.e. with and without ICV as covariate. Clearly, adding ICV as covariate here, is reducing effect size all ove

Re: [Freesurfer] ICV as covariate for controls vs. patients

The gammas do look different, but it is hard to tell whether they are, eg, changing sign. Not sure what you want me to comment on. On 7/24/18 2:17 PM, Martin Juneja wrote: External Email - Use Caution Just to add some more info here: The peak location of regions, X1 and X2, which I

Re: [Freesurfer] ICV as covariate for controls vs. patients

External Email - Use Caution Just to add some more info here: The peak location of regions, X1 and X2, which I found without including ICV as covariate are very close with the peak locations I found in Gamma_Without_ICV (~5.15), whereas Gamma_With_ICV is almost all over the brain (

Re: [Freesurfer] ICV as covariate for controls vs. patients

For noise compare the values in the rstd.mgh file, for effect size look in the gamma.mgh file On 07/24/2018 12:27 PM, Martin Juneja wrote: > > External Email - Use Caution > > Hi Dr. Greve, > > Thanks for your quick reply. Could you please give me more details how > can I check this whet

Re: [Freesurfer] ICV as covariate for controls vs. patients

External Email - Use Caution Hi Dr. Greve, Thanks for your quick reply. Could you please give me more details how can I check this whether its because of noise or its because of less CV difference? I am not sure what method/way is the best and commonly used to confirm these factor

Re: [Freesurfer] ICV as covariate for controls vs. patients

your results could have vanished after ICV correction for one of two reasons: the CV difference became less or the values became noisier (or a combination). So check in your data which one of those things happened. On 7/23/18 8:30 PM, Martin Juneja wrote: External Email - Use Caution

[Freesurfer] ICV as covariate for controls vs. patients

External Email - Use Caution Hello experts, I am interested in identifying regions of interest by comparing cortical volume (CV) between controls and patients. After including age and sex as my covariates, I identified regions X1 and X2, which showed significantly lower CV for pa

Re: [Freesurfer] ICV adjustment of volumes in longitudinal pipeline

Hi Tamir, ICV is fixed across time (derived from the template image), so that data can be compared directly, but for cross subject analysis you still need to adjust for ICV of course. Best, Martin > On 15. May 2018, at 03:19, Tamir Eisenstein wrote: > > > > Hello Freesurfer experts, > >

[Freesurfer] ICV adjustment of volumes in longitudinal pipeline

External Email - Use Caution Hello Freesurfer experts, If I want to analyze the volume difference of regions (2 time points) after performing all the 3 steps of the longitudinal pipeline, do I need to adjust each volume in the "long" directories to its specific "tp.long" ICV or ar

[Freesurfer] ICV correction for volume analysis

Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical

Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream

estimated long values when this assumption is > incorrect? > > Best regards, > Christian K Tamnes > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Martin Reuter > > Sent: 14 October 2014 17:23 > To: Freesu

Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream

on behalf of Martin Reuter Sent: 14 October 2014 17:23 To: Freesurfer support list Subject: Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream Hi Knut, the longitudinal stream assumes head size is fixed across time. That is why we report only one ICV (the one from the

Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream

Hi Knut, the longitudinal stream assumes head size is fixed across time. That is why we report only one ICV (the one from the within subject template) in all time points. If in your data heads are growing still, you can still use the longitudinal stream, but need to be carefully inspecting your

[Freesurfer] ICV for adolescent and young adult in longitudinal stream

Dear FreeSurfer export, I have used the longitudinal stream in FreeSurfer. However, when I extracted the ICV for adolescents and young adult, I get the same number for those subjects that are present at two-time points. Will registration to a common space cause the change in ICV? Can this chan

Re: [Freesurfer] ICV

to add to this, the registration it uses is performed on the whole head, so skull/skin/dura/fat/neck is included, which make the registration less susceptible to mis-registration due to lesions/atrophy/resection. n. On Wed, 2013-05-08 at 15:15 -0400, Douglas N Greve wrote: > I don't know, I don'

Re: [Freesurfer] ICV

I don't know, I don't think the test has ever been done. It probably depends upon how good the talairach registration is. doug On 05/08/2013 03:12 PM, Mohammed Goryawala wrote: > Hi, > > A follow up question pertaining to this issue for me is how good is > the measure of the ICV when dealing

Re: [Freesurfer] ICV

Hi, A follow up question pertaining to this issue for me is how good is the measure of the ICV when dealing with subjects having prior resections or significant atrophy. I am using FreeSurfer v5.1. Thank you M. Goryawala Post-Doctoral Associate Florida International University Miami, FL On Wed

Re: [Freesurfer] ICV

Thank you! Sent from my iPhone On May 8, 2013, at 8:17 AM, Douglas N Greve wrote: > > Hi Alejandra, I don't work with children, so I'll let someone else (Lilla? > Rudolph?) answer. > doug > ps. Please remember to copy the list on responses. Thanks! > > On 05/08/2013 01:19 AM, Alejandra Infan

Re: [Freesurfer] ICV

Hi Alejandra, I don't work with children, so I'll let someone else (Lilla? Rudolph?) answer. doug ps. Please remember to copy the list on responses. Thanks! On 05/08/2013 01:19 AM, Alejandra Infante wrote: > Thank you! I might have asked this at the training, but I am still not > clear on wheth

Re: [Freesurfer] ICV

It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV and/or Buckner et al. (2004) NeuroImage 23:724-738. "Basically, total intracranial volume is found to correlate with the determinant of the transform matrix used to align

[Freesurfer] ICV

Hi, I understand that ICV is an estimated measure based on a standard talairach transformation; however, I want to know how freesurfer is defining intracranial volume (i.e., is this a representation of everything within the cranium as the name implies or is it an estimate of total brain volume, whi

[Freesurfer] ICV calculation error?

Hi all, We use freesurfer 5.1.0 and we ran the recon-all on 100 subjects. We checked the talairach transform, skull strip the pial surfaces and the segmentations as suggested on Freesurfer Wiki. Everything seems to be fine, however, the ICV values from the stats/aseg.stats seem to be incorrect. T

Re: [Freesurfer] ICV measurement in freesrufer

See http://www.freesurfer.net/fswiki/eTIV On 06/12/2012 01:23 PM, Ayaz, Muhammad wrote: > > Dear all, > > How does the freesurfer calculate the ICV? By adding up all the > cortical and sub-cortical volumes including WM and GM and CSF? If so > does it also include cerebellum and brain stem? > > T

[Freesurfer] ICV measurement in freesrufer

Dear all, How does the freesurfer calculate the ICV? By adding up all the cortical and sub-cortical volumes including WM and GM and CSF? If so does it also include cerebellum and brain stem? Thanks Ayaz The information contained in this message and any attachments is intended only for the u

Re: [Freesurfer] ICV estimation

Note that a bug in the calculation of the supratentorial volume was recently identified (see archives), so if you want to use that measure you should get the fixed version of mri_segstats and regenerate the aseg.stats files. cheers, -MH On Fri, 2012-03-30 at 09:12 -0400, Bruce Fischl wrote: > Hi

Re: [Freesurfer] ICV estimation

Hi Gabriela it's hard to get a stable ICV measure from only a T1-weighted image, since you can't really distinguish bone from air. You can use supra tentorial, but you are testing a slightly different hypothesis (i.e. that hippocampal volume is changing faster than supratentorial volume). ch

[Freesurfer] ICV estimation

Dear all, I am working with FreeSurfer version 5.10 from 2 months. I am interested in hippocampus volume measurements and I want to normalize them with the intracranial volume. We have scanned about 4 times the same 2 healthy subjects (3T GE HDxt, 8 channel coil). 3D acquisitions were made

Re: [Freesurfer] ICV and regional brain volumes

Hi Heather, the ICV is mostly unrelated to the other volumetric measures. what do you mean that you are having problems getting ICV to fit correctly in your sample? doug Lugar, Heather wrote: > > We are having a difficult time getting the ICV to fit correctly in our > sample, but the segmention

[Freesurfer] ICV and regional brain volumes

We are having a difficult time getting the ICV to fit correctly in our sample, but the segmentions and parcellations look accurate. I believe that the ICV is generated from the talairach.xfm early on in the processing stream, but then further processing for segmentations/parcellations is done.

Re: [Freesurfer] ICV

Hi Dusan we typically do this for volume and surface area, but not for thickness, which is relatively independent of ICV. cheers, Bruce On Sat, 5 Nov 2011, Dusan Hirjak wrote: Dear Freesurfer experts, I am a beginner in using Freesurfer. I was wondering if ICV should be treated as a pote

[Freesurfer] ICV

Dear Freesurfer experts, I am a beginner in using Freesurfer. I was wondering if ICV should be treated as a potential confounder (such as age, education, chlorpromazine equivalents and duration of illness) in the statistical analysis of volumetric data/cortical thickness? Thanks in advanc

Re: [Freesurfer] ICV differences from version 5.0 to 5.1

good enough for freesurfer purposes, but clearly are not as good as v5.0. they seems sufficient for ICV as long as ICV is used as normalizer for, say, hippocampal volume, in a group study. the freesurfer ICV is not a very accurate absolute measure (see wiki on how its calculated). i suppose we

Re: [Freesurfer] ICV differences from version 5.0 to 5.1

Jon, The reason is that already in one step earlier in the pipeline, the nu-correct stage, a difference arises. See thread on "Differences in nu.mgz between v5.0.0 and v5.1.0" Cheers, Ed Hi, We have noticed differences in Talairach registration (and therefore ICV estimates) in some of our

Re: [Freesurfer] ICV smaller than the brain

Hi Jeff, it is the talairach.xfm file you need to check. The wiki says http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV 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

Re: [Freesurfer] ICV smaller than the brain

Hi jeff. Probably your Talairach registrations fail. There are several different maps. I don't remember which one is the one used for the eTIV but it is documented on the wiki. You probably looked at the wrong transforms. Best Martin Send from my phone On May 4, 2011, at 2:47 AM, Jeff Sadino

[Freesurfer] ICV smaller than the brain

Hello, I asked a question similar to this last year when working with FS 4.3.1, and I'm hoping that there is something new in FS 5 that can help. I am having a problem where a lot of my subjects' brains are larger than the eICV. In FS 4.3.1, it is happening in about 70/140 subjects, and in FS 5,

[Freesurfer] ICV error and talairach registration bad outputs...

Hi: In the image that I am sending attach, there exist a not exact talairach registration in the superior part of the brain... That difference produce an important error in the ICV, or not ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailin

Re: [Freesurfer] ICV and adjusting watershed

Hi Liesbeth if it's the eTIV you are looking at, that is computed from the determinant of the Talairach transform and is independent of the skull stripping. cheers Bruce On Fri, 7 Jan 2011 l.hoeks...@psy.umcn.nl wrote: > Dear Freesurfer users, > > We were suprised to find out in two cases tha

[Freesurfer] ICV and adjusting watershed

Dear Freesurfer users, We were suprised to find out in two cases that after adjusting watershed (because of skull that was left) and autorecon2 and autorecon3, the ICV was exactly the same as the ICV measured by pipeline--> autorecon-all. If we didn't adjust watershed in one case the skull was

Re: [Freesurfer] ICV differs systematically in repeated measurements

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

Re: [Freesurfer] ICV differs systematically in repeated measurements

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

Re: [Freesurfer] ICV differs systematically in repeated measurements

probably. The T2* will be different, so you'll have a different TE and different contrast, SNR and CNR On Mon, 20 Dec 2010, Anthony Dick wrote: > Would this problem also apply for fMRI or diffusion weighted scanning? > > On 12/20/10 10:41 AM, Bruce Fischl wrote: >> Hi Anthony, >> >> I don't thin

Re: [Freesurfer] ICV differs systematically in repeated measurements

Would this problem also apply for fMRI or diffusion weighted scanning? On 12/20/10 10:41 AM, Bruce Fischl wrote: > Hi Anthony, > > I don't think so. The problem is that the fundamental T1 contrast is > different at 3T than att 1.5T, which results in systematic biases. > > cheers > Bruce > On Mon,

Re: [Freesurfer] ICV differs systematically in repeated measurements

Hi Anthony, I don't think so. The problem is that the fundamental T1 contrast is different at 3T than att 1.5T, which results in systematic biases. cheers Bruce On Mon, 20 Dec 2010, Anthony Dick wrote: > This is just a thought, but is this issue mitigated to some degree if > you can show that

Re: [Freesurfer] ICV differs systematically in repeated measurements

This is just a thought, but is this issue mitigated to some degree if you can show that the regions in which you are interested meet a certain minimum signal to noise ratio? Or maybe a more stringent requirement would be necessary, such that the SNR of the ROIs don't differ significantly? Alwa

Re: [Freesurfer] ICV differs systematically in repeated measurements

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,

[Freesurfer] ICV differs systematically in repeated measurements

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

Re: [Freesurfer] ICV volume and 1.5T x 3.0T

Thanks Doug. I'll do it! TK On Fri, Aug 20, 2010 at 7:08 PM, Douglas N Greve wrote: > The ICV is not computed based on a sum of the volumes of individual > structures. It is a summary measure computed from the registration to > talairach space. See the wiki and Randy Buckner's paper for more

Re: [Freesurfer] ICV volume and 1.5T x 3.0T

The ICV is not computed based on a sum of the volumes of individual structures. It is a summary measure computed from the registration to talairach space. See the wiki and Randy Buckner's paper for more info. As for combining across field strengths, that would not be highly recommended. If you

[Freesurfer] ICV volume and 1.5T x 3.0T

Hi FS, I have two important doubts... Is it the CSF volume included in the ICV volume (aseg.stats)? Is it possible include in the same group patient acquired from 1.5T and 3.0T? Do you have an article about this topic? TK ___ Freesurfer mailing lis

Re: [Freesurfer] ICV meaning...

note that this is an estimate based on the talairach registration. We do not actually measure the icv Bruce Fischl wrote: > it is everything inside the skull (including brain, csf, etc...) > On Wed, 28 > Apr 2010, Gonzalo Rojas wrote: > > >> Hi: >> >> Which is the meaning of the Intracarani

Re: [Freesurfer] ICV meaning...

it is everything inside the skull (including brain, csf, etc...) On Wed, 28 Apr 2010, Gonzalo Rojas wrote: > Hi: > > Which is the meaning of the Intracaranial Volume (ICV) ?... it > includes only the brain, or also the skull ?... > > Sincerely, > > > Gonzalo Rojas Costa > Laboratory for Advan

Re: [Freesurfer] ICV meaning...

One is volume-based (Left-Cerebral-White-matter) and one is surface-based. Use the surfacse-based one. In the next version of FS, the volume-based one will no appear. doug Gonzalo Rojas wrote: > Hi: > >In aseg.stats file, appears "lh-cerebral-white-matter" and > "Left-Cerebral-White-matter

[Freesurfer] ICV meaning...

Hi: In aseg.stats file, appears "lh-cerebral-white-matter" and "Left-Cerebral-White-matter": which are the difference between both values?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las

[Freesurfer] ICV meaning...

Hi: Which is the meaning of the Intracaranial Volume (ICV) ?... it includes only the brain, or also the skull ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel

Re: [Freesurfer] ICV Error fs 4.3.1

It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: > Hello Doug, > > I loaded up the tkregister2 program and I think I see some poor > transformations. I've never really used it before though. Am I just > looking at wheth

Re: [Freesurfer] ICV Error fs 4.3.1

Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I

Re: [Freesurfer] ICV Error fs 4.3.1

Did you check the transform to make sure it is accurate? tkregister2 --s subject --fstal --surf It could be that the scaling is not good. I've seen this before (no solution yet). doug Jeff Sadino wrote: > Thanks Doug. That is very good news to hear! > > Maybe I spoke too soon about fixing the

Re: [Freesurfer] ICV Error fs 4.3.1

Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overal

Re: [Freesurfer] ICV Error fs 4.3.1

You just need to re-run segstats doug Jeff Sadino wrote: > Doug - > Thank you for your suggestion. I looked, and the > talairach_with_skull.lta file was unique to each subject. However, > the talairach.xfm file was actually a shortcut to > /apps/freesurfer3/subjects/fsaverage/mri/transforms/

Re: [Freesurfer] ICV Error fs 4.3.1

Doug - Thank you for your suggestion. I looked, and the talairach_with_skull.lta file was unique to each subject. However, the talairach.xfm file was actually a shortcut to /apps/freesurfer3/subjects/fsaverage/mri/transforms/talairach.xfm. This is because of some in-house legacy code that we use

Re: [Freesurfer] ICV Error fs 4.3.1

also note that if the subjects were processed by a prior version, then when re-run with v4.X, talairach.xfm will not get overwritten, as it is assuming it was edited. so you should check of talairach.xfm and talairach.auto.xfm are the same, and if not either re-run with -clean-tal, or just copy ta

Re: [Freesurfer] ICV Error fs 4.3.1

Can you check the talairach.xfm and the talairach_with_skull.lta to make sure that they are different across subject? Jeff Sadino wrote: > Hi Doug, > > Thanks for the quick reply. It just seems like an error that all 149 > subjects would line up exactly with the talairach transform (that > wou

Re: [Freesurfer] ICV Error fs 4.3.1

Hi Doug, Thanks for the quick reply. It just seems like an error that all 149 subjects would line up exactly with the talairach transform (that would give a determinant of 1.00?). The following commands I used from my script were: recon-all -sd /scratch/data431 -s 040002_S04 -autorecon1 *cod

Re: [Freesurfer] ICV Error fs 4.3.1

The ICV is *estimated* from the talairach transform. Did you happen to run recon-all with -notalairach? You can check that the talairach transforms are all different. doug Jeff Sadino wrote: > Hello, > I reconed 149 subjects using freesurfer 4.3.1 automatically using our > cluster. When I did

[Freesurfer] ICV Error fs 4.3.1

Hello, I reconed 149 subjects using freesurfer 4.3.1 automatically using our cluster. When I did asegstats2table, all 149 subjects had the exact same icv: # Measure IntraCranialVol, ICV, Intracranial Volume, 1948106.00, mm^3 Running mri_segstats manually, here is the beginning of the output:

Re: [Freesurfer] ICV/brain volume

al Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, January 11, 2010 10:08 To: Xiangchuan Chen Cc: 'Martin Reuter'; 'Michael Harms'; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ICV/brain volume Hi Xiangchuan, the cerebral gr

Re: [Freesurfer] ICV/brain volume

>> -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 volum

Re: [Freesurfer] ICV/brain volume

is 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:

Re: [Freesurfer] ICV/brain volume

5 > 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_a

Re: [Freesurfer] ICV/brain volume

ns. 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 > >

Re: [Freesurfer] ICV/brain volume

tats. > > 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

Re: [Freesurfer] ICV/brain volume

gt; 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 a

Re: [Freesurfer] ICV/brain volume

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

Re: [Freesurfer] ICV/brain volume

urface. 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 >> C

Re: [Freesurfer] ICV/brain volume

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 be

Re: [Freesurfer] ICV/brain volume

: [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 i

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 vent

[Freesurfer] ICV/brain volume

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 rig

Re: [Freesurfer] ICV for incomplete whole brain coverage

b" as to what is > necessary (in terms of brain/skull elements) for proper ICV values? > > Many Thanks for any comments, > Jenifer > > -Original Message- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Tuesday, November 17, 2009 12:05 PM > To:

Re: [Freesurfer] ICV for incomplete whole brain coverage

Hi Jenifer, how much is missing? If a substantial amount I would think things would fail, including the segmentation itself, but we very rarely do this. Bruce On Tue, 17 Nov 2009, Juranek, Jenifer wrote: > A colleague asked me to look at some T1s for possible Freesurfer analyses. > Unfortunat

[Freesurfer] ICV for incomplete whole brain coverage

A colleague asked me to look at some T1s for possible Freesurfer analyses. Unfortunately, several subjects do not have whole brain acquisitions (I know, quite unexpected and disappointing). Would it be possible to correct volumes of subcortical structures (which are covered by the acquisition) f

Re: [Freesurfer] ICV accuracy

Thanks, Bruce. That seemed to work well. Jared -- Jared Conley Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave., RF 394 P: 617.525.6238 Bruce Fischl wrote: Hi Jared, you can load the source (nu_noneck.mgz) and target (/autofs/space/

Re: [Freesurfer] ICV accuracy

Hi Jared, you can load the source (nu_noneck.mgz) and target (/autofs/space/tensor_004/users/fischl/dev/freesurfer/average/RB_all_withskull_2006-02-15.gca) volumes in tkregister2 with the transform (transforms/talairach_with_skull.lta) to check the alignment. cheers, Bruce On Thu, 12 Jun

[Freesurfer] ICV accuracy

FreeSurfer Community: A quick question for the group. Our lab was wondering if there is an easy way to assess the accuracy of the intracranial volume (ICV) measurement? Or is this not necessary (never any errors)? Thanks in advance, Jared -- Jared Conley Center for Neurological Imaging B

[Freesurfer] ICV / brain volumes

Hi. does it matter whether I use the total brain volumes or the ICVs from the aseg. stats in order to normalize individual brain structure volumes? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi