Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3

ter answer than that, other than to say look at the > segmentations and see if you think they are more accurate in one case > than the other. > > sorry > Bruce > On Sun, 23 Mar 2014, jh kim wrote: > > > Dear Prof. Fischl > > Thanks for the prompt response. > > &

Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3

; Hi Kim > > there are probably lots of little reasons for the differences. This is > always true for different versions, and the reason we never mix versions > > cheers > Bruce > On > Sun, 23 Mar 2014, jh kim wrote: > > > Dear FS lists > > When I measured subco

[Freesurfer] Difference in volumes btw 5.1 and 5,3

Dear FS lists When I measured subcortical GM volumes in the same subjects by using both version 5.1 and 5.3, I have observed a considerable difference in volumes between the two versions. For instance, please see the left thalamic volumes below. I cannot figure out why there is much difference bet

Re: [Freesurfer] CentOS 5.8

Dear Zeke Thanks for the advice Kim 2014-02-04 Z K : > Kim, > > Yes, the CentOS4 build of freesurfer is compatible with CentOS5. You can > download it from this page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/Download > > -Zeke > > On 02/03/2014 04

[Freesurfer] CentOS 5.8

Dear FreeSurferers Just a quick question. Is CentOS 5.8 fully compatible with FS 5.3? Thank you. Kim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

Re: [Freesurfer] P-value of interaction term in DODS

eady there with the y.ocn file), then do a post hoc test in SPSS, > matlab, etc > > doug > > > On 12/23/2013 03:39 AM, jh kim wrote: > > Dear Doug and experts > > > > Using DODS model in QDEC, I've found 2 significant clusters in > > whole-brain co

[Freesurfer] P-value of interaction term in DODS

Dear Doug and experts Using DODS model in QDEC, I've found 2 significant clusters in whole-brain cortical thickness analysis between controls and patients (2 group, 1 factor), controlling for the effect of age (one covariate). My question is how can I obtain p value for interaction term (group*age

Re: [Freesurfer] A question as to subcortical volumetric measurement

res as well as WM. VBM is a voxelwise > analysis which is registered to an atlas, modulated, and spatially > smoothed, all of which will have strong effects on the results. Maybe a > VBM expert on the list can chime in with more info. > > doug > > > > > On 11/05/

Re: [Freesurfer] A question as to subcortical volumetric measurement

ison and you probably smoothed by 10mm or so. Either of those > could have washed out the effect. Certainly a reasonable response is > that the FS analysis is for the entire ROI and and the VBM is voxelwise. > Hope that help.s > > doug > > > > On 11/03/2013 11:55 PM, jh kim wr

[Freesurfer] A question as to subcortical volumetric measurement

Dear Doug and experts I've analyzed structural changes of the subcortical GM by using both VBM (DARTEL in SPM8) and subcortical volumemetric measurement using FreeSurfer 5.1. While there is no significant volumetric difference between the groups in VBM (corrected p<0.05), FS results showed that so

Re: [Freesurfer] Finding a reference..

Thanks Alex. It would be of great help to me. Kim 2013/8/16 Alex Hanganu > Hi, > > I remember only finding articles that talked about the limitations of VBM. > Attached are some examples. > > Alex. > > > > > Le 15/8 9:37, jh kim a écrit : > > Dear ex

[Freesurfer] Finding a reference..

Dear experts Just a simple question. Is there a published study that showed a superiority of cortical thickness analysis (i.e., FreeSurfer) over VBM approach in assessing cortical grey matter changes in brain disorders? If so, please let me know. Thanks in advance for your help. Kim

Re: [Freesurfer] A question about coordinates

Thanks, Doug Kim 2013/7/29 Douglas Greve > Those are MNI305 coordinates. > doug > > > > On 7/28/13 9:58 AM, jh kim wrote: > > Dear experts > > I have a simple question. > To my knowledge, Freesurfer uses Talrairach coordinates. > After doing 1 perm

[Freesurfer] A question about coordinates

Dear experts I have a simple question. To my knowledge, Freesurfer uses Talrairach coordinates. After doing 1 permutations, I found that the resulting file *.sig.cluster.summary contained MNIX, MNIY, MNIZ coordinates. Are these coordinates in MNI space? Thank you in advance for your answer.

Re: [Freesurfer] Questions regarding QDEC

'--cache' flag option in mri_glmfit-sim command? Thank you in advance for your help. Kim 2013/7/11 Douglas N Greve > > On 07/09/2013 10:07 PM, jh kim wrote: > >> Dear Prof. Greve >> >> I have additional (and probably silly) questions. >> >> 1) I

Re: [Freesurfer] Questions regarding QDEC

mri_glmfit command)? Thank you for your kindness Kim 2013/7/9 Douglas N Greve > > On 07/07/2013 01:36 PM, jh kim wrote: > > Dear FreeSurfer experts... > > > > Please be patient with a newbie's questions. > > For the first time, I'm trying to analyze b

[Freesurfer] Questions regarding QDEC

Dear FreeSurfer experts... Please be patient with a newbie's questions. For the first time, I'm trying to analyze between-group differences in cortical thickness (controls vs. patients) by using FS 5.1.0 and QDEC. I've read through the online manual and mailing lists; however, I cannot figure out