[Freesurfer] Reconstruct the white and pial from a single brain slice

External Email - Use Caution Dear, I tried to reconstruct the white and pial surface from a sinlge brain slice (not MRI, it's a histology slice that converted to a nifti file) but failed when using the mris_make_surface. The white matter and grey matter were segmented by in-ho

[Freesurfer] mris_preproc error: no source hemi specified

External Email - Use Caution Dear FreeSurfer experts, I need your help. I am trying to run mris_preproc --fsgd in order to see the effect of cortical volume on velocity, accounting for the effects of eTIV in the analysis. My .fsgd file looks like GroupDescriptorFile 1 Title Vel_v

[Freesurfer] Question glm analysis g4v0

External Email - Use Caution Hello FreeSurfer Developers, I am performing a GLM analysis to assess cortical thickness between 4 groups, without any covariates. I followed exactly what is on the wiki https://secure-web.cisco.com/1VuhMA49mKmIDKH_rGPy4c67MdbjL6bNv2i_WwNDwvMA5-MXr

Re: [Freesurfer] Virtual Machine (VM_67) password request

External Email - Use Caution Hi there, Thank you for your email. Do you need any info from me for this? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of daedalu...@aol.com Sent: Thursday, February 17, 2022 12:41 PM To: freesurfer@nmr.mg

Re: [Freesurfer] FreeSurfer Issue

External Email - Use Caution Dear Anna, You should use 'setenv' (for tcsh and related shells) or 'export' (for BASH) when defining environment variables, as listed here: https://secure-web.cisco.com/10e4snIgzUxrLukGTpLLWEbQgYzRweBims_84Fu3AbnlVO2lbkQLoCTO39OnIq0oZVMIuqLuSi-

Re: [Freesurfer] FreeSurfer Issue

External Email - Use Caution Hi there, For these, my terminal says ""no such file or directory" From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim Schäfer Sent: Thursday, February 17, 2022 2:10 PM To: Freesurfer support list Subject:

Re: [Freesurfer] Virtual Machine (VM_67) password request

External Email - Use Caution Sending the info to your email shortly. - R. From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of daedalu...@aol.comSent: Thursday, February 17, 2022 12:41 PMTo: freesurfer@nmr.mgh.ha

[Freesurfer] Fw: Freeview problem - can't see surfaces, hidden behind volumes

External Email - Use Caution Hi there, I am having a weird problem with freeview… When l load some volumes and some surfaces together, I can’t see the surfaces because they are hidden ‘behind’ the volumes. They normally sit on top, but now I can only see them if I toggle off

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

Hello Doug, just following up on my questions below on how/if I can correct for multiple comparisons with PVR. Thanks again. Best, Asim From: Dhungana, Asim Sent: Monday, February 14, 2022 11:45 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_glmfit

Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

It sounds like a remote display issue. Are you connecting from a Windows machine? If so what x-term software do you use? Ruopeng On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones mailto:h.dempseyjo...@uq.edu.au>> wrote: External Email - Use Caution Hi there, I am having a weird p

Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and  ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the

Re: [Freesurfer] Freesurfer Virtual Box VM (ubuntu 18) - developer account

External Email - Use Caution Sending the into to your email shortly. - R. On Feb 17, 2022, at 16:50, Haniya Saleh wrote:External Email - Use CautionHi Freesurfer team, We are trying to setup Freesurfer on an Ubuntu 18 Virtual Box VM. We are

Re: [Freesurfer] FW: Problems with recon for manually fixed Talairach

oh, I see what is happening now. wow, I had no idea that it deleted the existing xfm and reran the tal if the check failed. sorry, it should not be that way. I'll change it for the next version. In the meantime, you can proceed with -notal-check as you suggest. On 2/16/2022 1:33 PM, Goeckner,

Re: [Freesurfer] SAMSEG mesh format and content

On 2/16/2022 3:35 PM, Martin Kavec wrote: External Email - Use Caution Hi all, previous question from Florent triggered my interest in SAMSEG and I am running now couple of cases to see what it gives. I would like to ask * SAMSEG can also output a mesh. How is the mesh stored in

Re: [Freesurfer] Longitudinal Stream Error

fsaverage should not be empty. Maybe it is a link to an empty folder? It should point to $FREESURFER/subjects/fsaverage. You should not mix the streams in this way (insert Ghost Busters joke here) On 2/16/2022 4:33 PM, Willett, Andrew Sunday wrote: Dr. Greve, I don't believe that file exists-

Re: [Freesurfer] Reconstruct the white and pial from a single brain slice

Sorry, the surfaces are 3D structures, it's not going to work on a 2d slice On 2/17/2022 8:47 AM, 陆玉恒 wrote: External Email - Use Caution Dear, I tried to reconstruct the white and pial surface from a sinlge brain slice (not MRI, it's a histology slice that converted to a nifti file)

Re: [Freesurfer] mris_preproc error: no source hemi specified

Did you specify a hemi? If you run it with --help it will give you docs. You can also  find them on line. You should also send the command line On 2/17/2022 9:23 AM, Koustav Chatterjee wrote: External Email - Use Caution Dear FreeSurfer experts, I need your help. I am trying to run m

Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

External Email - Use Caution Hi there, Here's an issue that keeps coming up: source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh Could you help with this? From: freesurfer-bo

Re: [Freesurfer] FreeSurfer Issue

External Email - Use Caution Hi, Sorry but this did not fix the issues- could I ask you to help with Freesurfer? I tried to get it work many times, with no success and what you recommended also did not work. Thank you. From: freesurfer-boun...@nmr

Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

External Email - Use Caution - Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. - ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some exten

Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

Hi Anna Where did you install FreeSurfer? That is where the env variable FREESURFER_HOME should point. What does: ls $FREESURFER_HOME show you? Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Pusok, Anna Sent: Thursday, February 17, 2022 6:40 PM To: Freesurfer support list

Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

Hi Edan Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two? Cheers Bruce From: freesurfer-boun...@nmr.mgh.har

Re: [Freesurfer] FreeSurfer Issue

External Email - Use Caution Hello Anna, You could try the bash shell commands below … freeview should open an empty window. Those commands are documented for the bash shell and also csh/tcsh shells on the help page, https://secure-web.cisco.com/1HXGi2MgGyKrnZsUEDporX-UQ3IrQRAR1