[Freesurfer] shift to account for hemodynamic response

Dear experts, I just have switched from SPM to Freesurfer. I am wondering if in FSFAST analysis, we require to shift the regressors in time to account for the delay in hemodynamic response? Thanks ___ Freesurfer mailing list

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Thanks, Bruce. >From that, I got thickness data (vertex#, location x/y/z, thickness value). But, amount and location of vertex are different among subjects. As far as i understand, it is the subject space, not common space. is that right? If so, how can i get the thickness values in common space

Re: [Freesurfer] thresh definition

Thank you so much, Dr. Greve. My last question, are these t-tests corrected or uncorrected? On Tue, Feb 6, 2018 at 9:03 PM, Douglas Greve wrote: > thresh = -log10(p-value threshold), so it kind of means the number of > decimal points but is more general > > On

Re: [Freesurfer] thresh definition

thresh = -log10(p-value threshold), so it kind of means the number of decimal points but is more general On 2/6/18 9:13 PM, Ashley Cole wrote: Dear experts, Could you please let me know what "thresh" means in funcroi-config. Like in general, sig=2, does this refer to the number of decimal

[Freesurfer] thresh definition

Dear experts, Could you please let me know what "thresh" means in funcroi-config. Like in general, sig=2, does this refer to the number of decimal points, here p<0.01? And I want the p-value less than 0.1, does this mean that I need to assign threshold of 5? Thanks

[Freesurfer] brainGraph (graph theory analysis in R) major release: v2.0.0

Dear Freesurfer users, I am pleased to announce the 2nd major release of my R package for graph theory analysis of brain MRI data, "brainGraph". The main page on CRAN is at: https://cran.r-project.org/ web/packages/brainGraph/index.html The GitHub repository is at:

Re: [Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer

I think the HCP CCF protocol is a good start: http://protocols.humanconnectome.org/ Peace, Matt. From: on behalf of Colm Connolly Reply-To: Freesurfer support list Date: Tuesday, February 6, 2018

Re: [Freesurfer] Removing labels after extending parcellation into white matter

Hi Doug, That's very helpful, thank you! I have 2 follow-up questions though: 1. Is it possible to merge the cortical label (e.g. label 1001 ctx-lh-bankssts) with its corresponding label that extends into the WM (e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may not give

Re: [Freesurfer] Using subject specific template, atlas, & TPM

Take a look at the bottom of this page: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > On Feb 6, 2018, at 2:04 PM, Saturne Fox wrote: > > Hey ! > > Is it possible not to receive the mails

Re: [Freesurfer] Using subject specific template, atlas, & TPM

Hey ! Is it possible not to receive the mails anymore ? Best regards, Antoine Le 11 janv. 2018 18:27, "Ramesh Babu" a écrit : > Dear experts, > > I have analysed T1 data using Freesurfer. Now we have created atlas, > template & tissue probability map using

[Freesurfer] PROGRAMMER/ DATA ANALYST II

PROGRAMMER/ANALYST II G. OPPENHEIMER CENTER FOR NEUROBIOLOGY OF STRESS AND RESILIENCE UNIVERSITY OF CALIFORNIA, LOS ANGELES Background: The G. Oppenheimer Center for Neurobiology of Stress and Resilience (Mayer Lab) in the Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen

[Freesurfer] Multiple regression FreeSurfer

Hi, I am interested in correlating cortical volume measures with behavioral data X1, after regressing out the effect of age and sex. For that I ran following commands: mri_glmfit --y lh.X1.CV.15.mgh --fsgd X1.fsgd dods --C Corr-X1-cor.mtx --surf fsaverage lh --cortex --glmdir lh.X1_CV.glmdir

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

good, but that is not a long-term solution. I don't know why that is working but it does not work when you run it from the shell. There must be some kind of permission or id change when you run it from the shell. I don't know. On 2/6/18 8:55 AM, Yagmur Ozdemir 19 wrote: > That works, thank

[Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer

Hi everybody, I’m endeavoring to help a researcher come up with a protocol which might be “optimal” (in some sense) for use with FreeSurfer. I’ve not really used FreeSurfer much hence my lack of familiarity with what the recommended sequences are for use with FreeSurfer. Having searched

[Freesurfer] Gray matter mask

Hello FS team, I am new to FS and using version 5.3 on a Mac. I have minimal programming background and this might be a very easy question, however I was not able to find a similar one in the archive. I have T1 MRI images from multiple subjects and I need to extract the brain gray matter

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

That works, thank you! Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] How to compile FreeSurfer with CUDA?

I am using Mageia 6 with CUDA and gcc installed from official Mageia-repositories: [mer@thalamus ~]$ uname -a Linux thalamus 4.14.16-server-1.mga6 #1 SMP Wed Jan 31 21:02:35 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux [mer@thalamus ~]$ nvcc --version nvcc: NVIDIA (R) Cuda compiler driver Copyright