[Freesurfer] wm.mgz edits amygdala hippocampus cerebral cortex

Dear all Freesurfer users, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip errors

[Freesurfer] wm.mgz edits

Dear all, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip errors, intensity nor

[Freesurfer] Design matrix for local gyrification index in QDEC

Dear all, I have a quick question regarding the appropriate design (DOSS, DODS, SOSS, SODS) to be used with QDEC when comparing LGI values for 2 groups (patients and healthy controls). I have noted that a number of publications have used DODS when comparing LGI values between 2 groups while contro

[Freesurfer] DODS and DOSS

Dear Freesurfer experts, I have a quick question regarding the appropriate design (DOSS or DODS) to be used with QDEC when comparing 2 groups for cortical thickness and LGI values. So far I have used DODS first to look for an age-cortical thickness interaction in both groups. I used the real ages

Re: [Freesurfer] DODS and DOSS

S and you're interested in > the diff bet groups, then first test for an interaction between group and > covariate. If that is not significant, then use DOSS > > On 6/20/17 5:05 AM, marco mcsweeney wrote: > > Dear Freesurfer experts, > > I have a quick question regarding

Re: [Freesurfer] DODS and DOSS

? Thank you so much again. Best wishes Marco On Tue, Jun 20, 2017 at 3:29 PM, Douglas Greve wrote: > > > On 6/20/17 10:14 AM, marco mcsweeney wrote: > > Dear Doug, > > thank you so much for getting back to me on this. > > I am using Freesurfer version 5.3 with QDEV

Re: [Freesurfer] DODS and DOSS

Dear Doug, OK thank you so much for all of your help. Best wishes Marco On Tue, Jun 20, 2017 at 3:58 PM, Douglas Greve wrote: > > > On 6/20/17 10:43 AM, marco mcsweeney wrote: > > Dear Doug, > > thank you. > > I will go ahead with DOSS through the command l

Re: [Freesurfer] DODS and DOSS

sance factor in the analysis. Thank you so much again for your time. Best wishes Marco On Tue, Jun 20, 2017 at 3:58 PM, Douglas Greve wrote: > > > On 6/20/17 10:43 AM, marco mcsweeney wrote: > > Dear Doug, > > thank you. > > I will go ahead with DOSS through the comm

Re: [Freesurfer] DODS and DOSS

t; design matrix not the contrast matrix) > > On 6/20/17 11:58 AM, marco mcsweeney wrote: > > Dear Doug, > > I have a few final questions, my apologies. > > The study I am working on is a retrospective study, which is not ideal. As > a result, although all of the individ

Re: [Freesurfer] DODS and DOSS

Dear Doug, thanks again. Will look into which is the best for LGI (if any). Best wishes Marco On Tue, Jun 20, 2017 at 7:48 PM, Douglas Greve wrote: > > > On 6/20/17 2:42 PM, marco mcsweeney wrote: > > Dear Doug, > > thanks again. I used mri_info --sres orig.mgz (T1.

[Freesurfer] viewing mri_glmfit FDR corrected results

Dear FreeSurfer experts, I ran my group analysis using mri_glmfit and found a number of significant clusters showing cortical thickness differences between 2 groups. I used tksurfer to visualize the results and used FDR to correct for multiple comparisons. My question is about how do I correctly

Re: [Freesurfer] viewing mri_glmfit FDR corrected results

i. Set > --annot aparc. Set --sum to the output summary file. This should give you > something similar to the output of mri_glmfit-sim. > > On 6/29/17 4:29 PM, marco mcsweeney wrote: > > Dear FreeSurfer experts, > > I ran my group analysis using mri_glmfit and found a number of

[Freesurfer] HELP! FDR vs clusterwise correction for multiple comparisons

Dear Doug and Bruce I have a couple of questions regarding multiple comparison correction. Any help with this would be really appreciated! I am conducting a cortical thickness analysis between 2 groups (patients vs controls). My understanding is that first I should check for an age-cortical thi