[Freesurfer] Freeview - Load custom overlay from terminal

External Email - Use Caution Dear FS experts, I’m trying to load a surface with a custom overlay directly from the terminal using the sub-option “overlay_custom” but it returns “Unrecognized sub-option flag ‘overlay_custom’”. I checked the source code on GitHub and found the fla

[Freesurfer] VM ubuntu developer password

External Email - Use Caution Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on t

Re: [Freesurfer] Longitudinal Stream Problem

I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote: External Email - Use Caution Hi Douglas, OK I just uploaded the base separately.  danielianbase.tar.gz  I thought it was part of the original bundle.  Sorry! Laur

Re: [Freesurfer] How to get access to the coordinate data of specified area

In general, the FS license is very general, so I imagine that you can use it with your project. You can get centroids from aseg segmentations with mri_segcentroids On 6/17/2020 11:02 PM, Chen Yu wrote: External Email - Use Caution Hello, I found FreeSurfer can segment brain areas au

Re: [Freesurfer] Freeview - Load custom overlay from terminal

Hi Ricardo, The way you use the flag is correct. But have you made sure that you were actually running the latest version that you built? You can check freeview’s build time from About menu. Best, Ruopeng > On Jun 18, 2020, at 4:15 AM, Loucao, Ricardo wrote: > >External Email - Use

[Freesurfer] recon-all for macaque brain

External Email - Use Caution Hi there, I'm running freesurfer to analyze macaque brain. Since the monkey brain is much smaller than human brain. We use 0.5*05* 05mm to scan the monkey brain. Is there anyway I can avoid downsampling the scan resolution to 1*1*1mm by recon-all?

Re: [Freesurfer] recon-all for macaque brain

Is your voxel size really that isotropic? You can try using the -hires option On 6/18/2020 10:40 AM, Minqing Jiang wrote: External Email - Use Caution Hi there, I'm running freesurfer to analyze macaque brain. Since the monkey brain is much smaller than human brain. We use 0.5*05* 

Re: [Freesurfer] VM ubuntu developer password

External Email - Use Caution Hello Amie, I have just sent the password to your private email. - R. On Jun 18, 2020, at 08:57, FAIRS Amie wrote:External Email - Use CautionDear Freesurfer mailing list, I have just downloaded the virtual ma

Re: [Freesurfer] VM ubuntu developer password

External Email - Use Caution Hello everyone, I have been sent the VM ubuntu password. But in case this is useful for others – at least on my laptop the ubuntu distribution is using a US/international QWERTY keyboard. My laptop has an AZERTY keyboard (French) and so I had some p

Re: [Freesurfer] Longitudinal Stream Problem

External Email - Use Caution Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.g

Re: [Freesurfer] VM ubuntu developer password

External Email - Use Caution I have also just ran into this issue. Can someone send me the password as well? Thansk, Cyrus Cyrus Sarosh [1587656965587] Research Area Specialist Intermediate Department of Radiology Functional Neuroimaging, Cognitive and Mobility Laboratory Domi

Re: [Freesurfer] VM ubuntu developer password

External Email - Use Caution Ok Cyrus - I have just sent it to your email. - R. Sarosh, CyrusJune 18, 2020 at 16:02 External Email - Use Caution I have also just ran into this issue. Can someone send me the password as we

[Freesurfer] Visualization of FreeSurfer overlays in the HCP format

Dear FreeSurfer community, I would like to be able to display OVERLAY files generated in FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states in their documentation (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoIma

Re: [Freesurfer] How to get access to the coordinate data of specified area

External Email - Use Caution Thank you very much!!! and could you tell me if there have a dev version document? I only find a document using command line. bests. On Thu, Jun 18, 2020 at 9:16 PM Douglas N. Greve wrote: > In general, the FS license is very general, so I imagine t

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

External Email - Use Caution What kind of data does one display in an “OVERLAY” file? Matt. From: on behalf of "Katsumi, Yuta" Reply-To: Freesurfer support list Date: Thursday, June 18, 2020 at 5:43 PM To: Freesurfer support list Subject: [Freesurfer] Visualization of FreeSu

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

Hi Matt, For instance, I have a statistical map (e.g., showing magnitude of functional connectivity at each vertex) that has been computed in 16k fsaverage space that I want to display on a fs_LR surface. I was wondering if there’s a way to convert this file (which is in .mgh extension now) to