Re: [Freesurfer] Regarding: Group analysis of WMHs

Yes, CVS should work On 06/09/2017 05:13 PM, Elijah Mak wrote: > Thanks Doug. I will look those tools up! > > Regarding the spatial normalisation, would mri_cvs_register be suited > for this purpose? Specifically, using the —mni option so that I still > run the eventual comparisons in MNI space

Re: [Freesurfer] Regarding: Group analysis of WMHs

Thanks Doug. I will look those tools up! Regarding the spatial normalisation, would mri_cvs_register be suited for this purpose? Specifically, using the —mni option so that I still run the eventual comparisons in MNI space? Best Wishes, Elijah  On 9 June 2017 at 21:42:44, Douglas N Greve (gr.

Re: [Freesurfer] methodological questions for manuscript

Great! Thank you Bruce, Heidi On 6/9/17, 9:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: >that sounds reasonable to me. > >good luck >Bruce >On Fri, 9 Jun 2017, Jacobs H (NP) wrote: > >> Hi! >> >> For my manuscript, the journal wants me to answer some question

Re: [Freesurfer] Regarding: Group analysis of WMHs

On 06/09/2017 04:32 PM, Elijah Mak wrote: > Hi Doug, > > I am referring to a rather old thread where you have provided some > interesting suggestions to perform group-wise analysis of WMHs. I am > trying to do something similar in patients and controls. First, > mri_binarize was used to extrac

Re: [Freesurfer] Regarding: Group analysis of WMHs

Hi Doug, I am referring to a rather old thread where you have provided some interesting suggestions to perform group-wise analysis of WMHs. I am trying to do something similar in patients and controls. First, mri_binarize was used to extract the individual WMH volumes from aseg.mgz. These volum

Re: [Freesurfer] methodological questions for manuscript

that sounds reasonable to me. good luck Bruce On Fri, 9 Jun 2017, Jacobs H (NP) wrote: Hi! For my manuscript, the journal wants me to answer some questions on the methods that I used and I want to make sure I am giving correct information on how FreeSurfer calculates hippocampal volumes. Wou

Re: [Freesurfer] Cortical thickness_Group analysis

I can't open that image (what is .odp?). The red/yellow is a positive contrast, blue/cyan is negative contrast. The contrast depends on your contrast matrix. Assuming that you have MS-Heal, the red/yellow is MS>Healthy. It is thresholded at an UNCORRECTED level of p<.01 (-log10(.01) = 2). F is

Re: [Freesurfer] Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis

here it is again. The responses are embedded On 06/09/2017 09:51 AM, Douglas Greve wrote: > > > > On 6/6/17 11:50 AM, Tamara Tavares wrote: >> Hello, >> >> I have ran my data through the default recon-all processing stream >> and am planning on analyzing ventricular volume and cortical >> thick

Re: [Freesurfer] Outputs from 5.3 to 6.0

Dear Manuel, I would chime in with my current experience with transfering v5.3 reconstructions to v6.0: The wm segmentation results (and therefore white/pial surfaces, apart from other things) are different between versions, especially in ambiguous areas and especially if there is a difference

Re: [Freesurfer] Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis

Hi Douglas, The message stream indicates you replied to my email but I don't see your response in the email thread. I am not sure what happened. Can you please reply again? Thank you, Tamara On 6/6/17 11:50 AM, Tamara Tavares wrote: > Hello, > > I have ran my data through the default recon-all

Re: [Freesurfer] testing FS installation - apparent cursor RAS coordinate mismatch?

It is very likely that the bert used in that screencapture is different than the bert subject ultimately shipped with the freesurfer v6 release. -Zeke On 06/08/2017 02:53 PM, Antonio Algaze Beato wrote: > Hello, > > I just installed FS 6 (mac OS) and followed Examples 1, 2, 3 and 4 under > the

Re: [Freesurfer] FW: F and p- values for non sig findings {Disarmed}

Those will have the vertex-wise p-values. You can read them in to matlab with the MRIread() command. On 6/7/17 8:18 AM, Lim, Lena wrote: Dear Doug, Thanks very much for your reply. Sorry, I couldn’t read the files—would they show the non-significant F and p values as I would find in the su

Re: [Freesurfer] How to process ANCOVA with age as covariate

That contrast vector (0 0 1 -1) will compute the interaction between group and age On 6/6/17 9:25 PM, Gwang-Won Kim wrote: Hello FreeSurfer Developers, To compare cortical thickness between groups, I want to process analysis of covariance (ANCOVA) adjusting for age. When "mri_glmfit" proces

Re: [Freesurfer] Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis

On 6/6/17 11:50 AM, Tamara Tavares wrote: Hello, I have ran my data through the default recon-all processing stream and am planning on analyzing ventricular volume and cortical thickness. I was wondering whether I need to use the Qdec to complete the ventricular volume and cortical thicknes

Re: [Freesurfer] How to do a regular GLM in 2 groups with 2 times

have you looked at this? https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis On 6/6/17 11:28 AM, llk...@sina.com wrote: Dear FS Experts, I want to measure the thickness difference between two groups, control and experimental group. And every subject scaned twice. I look at the page: htt

Re: [Freesurfer] mris_anatomical_stats and cortical thickness

Have you tried to view your label on the individual subject? If your original analysis was on cortical thickness, then there will be a *ocn*.dat file in the output with the values for each input subject and each cluster On 6/6/17 10:14 AM, Taylor Hilton wrote: Hi all, I’m trying to extract

Re: [Freesurfer] Cortical thickness_Group analysis

Hi Ali, the FSGD and contrast matrices look right as do your command lines. What is the problem? On 6/8/17 1:40 PM, Ali Radaideh wrote: Dear Douglas, Can I check with you if you have received my reply below to your question?? Thanks, Ali On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh

Re: [Freesurfer] Outputs from 5.3 to 6.0

all the edits will be taken into account regardless of what command line args you use On 6/9/17 3:08 AM, Manuel Delgado wrote: Dear all, Regarding this issue: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51931.html we have the same situation. We are going to reprocess data

[Freesurfer] Outputs from 5.3 to 6.0

Dear all, Regarding this issue: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51931.html we have the same situation. We are going to reprocess data previously processed with FS 5.3. If we proceed with *recon-all -all *will all the edits be taken into account (i.e. skull strip, co