[Freesurfer] Binary Mask Overlay

Hi FreeSurfer Team, I used QDEC to do a group analysis and from that I generated a surface-based mask using the command "mri_binarize --i sig.mgh --min 3 --o mask.mgz" Ultimately, I would like to overlay this mask on an individual subject (other than the fsaverage "lh.inflated" surface). Usin

[Freesurfer] Monte Carlo threshold p-values

External Email - Use Caution Hello FreeSurfer experts, In the FreeSurfer wiki page regarding multiple comparisons (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons ) under "Simulation

[Freesurfer] Monte Carlo simulation - vertex wise threshold question

External Email - Use Caution Hi FreeSurfer experts, I am trying to understand the Monte Carlo Z simulation in FreeSufer (mri_glmfit-sim) and have a question about the vertex wise /cluster forming threshold. In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set

[Freesurfer] hardware upgrade affect Freesurfer?

External Email - Use Caution Hi FreeSurfer Experts, Would upgrading computer hardware affect FreeSurfer output? We are using FreeSurfer version 5.3-HCP and we are considering upgrading our server. It will have the same operating system but different computer specs (memory, cpu

[Freesurfer] PetSurfer reference region

External Email - Use Caution Hello PetSurfer experts, We are using the cerebellum cortex as our reference region, but noticed that the SUVR values for lh/rh cerebellum cortex do not have a value of 1 (which is what we were expecting). The actual SUVR values are 1.31 for the lh a

Re: [Freesurfer] PetSurfer reference region

PetSurfer reference region To: Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" I cannot replicate this in either v6 or v7beta. Can you send the terminal output? On 3/5/2020 1:32 PM, Dincer, Aylin wrote: > &

Re: [Freesurfer] PetSurfer reference region

l compute the scaling from all 6 whereas the gtm.stats file is only from the first frame. Try running it with a single frame. Note that the gtm.nii.gz will have all the frames for each ROI. On 3/6/2020 3:56 PM, Dincer, Aylin wrote: > External Email - Use Caution > > Thanks

[Freesurfer] tkmedit in FreeSurfer 7.0

External Email - Use Caution Hi FreeSurfer Experts, We are unable to use tkmedit using FreeSurfer 7.0 (centos 7). In the .xdebug_tkmedit file, it outputs the following error: "Tcl_Init returned 1: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/t

[Freesurfer] FreeSurfer 7.1 patch question

External Email - Use Caution Hi FreeSurfer Experts, Is there a tentative date when the FreeSurfer 7.1 patch and docker implementation is going to be released? Thanks! Aylin _ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging C

[Freesurfer] freesurfer flag for multiple edited volumes

External Email - Use Caution Hello FreeSurfer Experts, If I need to manually edit both the brainmask.mgz and the wm.mgz in a FreeSurfer, what are the recommended flags when rerunning recon-all with the edits (-all, -autorecon2, etc)? Or is it recommended to run an edited volume

Re: [Freesurfer] freesurfer flag for multiple edited volumes

lin Aylin Dincer aylin.din...@wustl.edu<mailto:aylin.din...@wustl.edu> From: Nolan, Jackson [mailto:jnol...@mgh.harvard.edu] Sent: Wednesday, January 13, 2021 10:31 AM To: freesurfer@nmr.mgh.harvard.edu; Dincer, Aylin Subject: Re: freesurfer flag for multiple edited volumes * External Email -

[Freesurfer] Research Assistant Positions at Washington University School of Medicine

External Email - Use Caution The Benzinger Imaging Core Laboratory at Washington University School of Medicine is looking for full-time Research Assistants (multiple openings available!) to work with us on magnetic resonance imaging and positr