Re: [Freesurfer] Save (any/open) path in freeview

I don’t think freeview can save a path. I will add an option to do that. Ruopeng > On Aug 10, 2024, at 10:27 PM, Marianne Duyck wrote: > >External Email - Use Caution > > Dear freesurfer experts, > > I am currently using freeview 7.2.0. I want to compare

Re: [Freesurfer] freeview colormap for volumes

You can create your own color table file and put it in ‘luts’ folder under your FS home directory. There are a few stock color table files in that folder. You can copy and modify one of them to your own. The current color table does not support transparency, though. Ruopeng On Jul 8, 2024, at

Re: [Freesurfer] Inquiry About Using Freeview's ROI/Voxel Edit Tool on Surface File

You can use Path and Custom Fill tools for surface to create/edit ROI labels. The tools can be accessed from the second row of the surface toolbar. Ruopeng On Jun 27, 2024, at 5:08 AM, Dai, Y. (Yuxuan) mailto:yuxuan@donders.ru.nl>> wrote: External Email - Use Caution

Re: [Freesurfer] Freeview problems

Can you confirm where your license file is? Ruopeng On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) mailto:a.sav...@student.maastrichtuniversity.nl>> wrote: External Email - Use Caution To whom it may concern, I am using freesurfer package on a MacBook Pro (macOS

Re: [Freesurfer] command line options to control appearance in timecourse window

Hi Sebastien, Currently there is no such option from the command-line. I will add it. Ruopeng On Mar 26, 2024, at 4:57 PM, Proulx, Jean Sebastien mailto:jspro...@mgh.harvard.edu>> wrote: Dear Fresurfers, I'm visualizing multiple timecourses using the -timecourse window in freeview

Re: [Freesurfer] Freeview crashes when trying to load volumes

I would also check if the license file is installed properly. On Jan 15, 2024, at 7:06 PM, fsbuild mailto:fsbu...@contbay.com>> wrote: External Email - Use Caution It would help for us to know what your machine is running, e.g., linux or MacOS (Intel or Silicon Mac) - and what the ve

Re: [Freesurfer] Freeview not showing output

wrote: External Email - Use Caution Hi Ruopeng, Thank you for your quick reply! When running glxgears I just see a blank window. Sincerely, Zeena Shawa From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harva

Re: [Freesurfer] Freeview not showing output

What if you run glxgears command? Do you see 3D spinning gears or just a blank window? Ruopeng From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Shawa, Zeena Sent: Wednesday, January 3, 2024 9:17:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject

Re: [Freesurfer] Question about Freesurfer

It sounds like an openGL rendering issue. If you run glxgears command, do you see a blank window or spinning 3D gears? Ruopeng On Nov 6, 2023, at 12:37 PM, Mahdi Babaei mailto:mahdibabai...@gmail.com>> wrote: External Email - Use Caution Hi Paul, Thank you for your response.

Re: [Freesurfer] Freesurfer crash when loading "volume" surf

Can you load a MRI volume? From the crash report, it seems to be a system related issue that triggered the crash. Ruopeng On Oct 26, 2023, at 8:42 PM, Mirsol Choi mailto:mir...@ualberta.ca>> wrote: External Email - Use Caution Hi there, I have processed a t1 image using rec

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

Did you load everything from the command-line? Or did you load the surface first and then load the volume from the GUI. Again, would be very helpful if you can send us the exact volume and surface files so we can diagnose. On Oct 16, 2023, at 10:47 AM, Andrei Bieger mailto:andreibie...@gmail.c

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

Would it be possible to send us the volume and the surface files? If the volume geometric info from the surface is missing or wrong, it would be unlikely to align with the volume. Ruopeng On Oct 15, 2023, at 11:06 AM, Andrei Bieger mailto:andreibie...@gmail.com>> wrote: Ex

Re: [Freesurfer] voxel-specific opacity

External Email - Use Caution Hi Sebastien, Freeview does not support voxel-specific alpha channel. You can only apply a uniform opacity. Ruopeng On Sep 8, 2023, at 9:16 AM, Proulx, Jean Sebastien mailto:jspro...@mgh.harvard.edu>> wrote: External Email - Use C

Re: [Freesurfer] Use freeview to visualize white and pial surface

s tool? Thank you so much. At 2023-08-08 21:27:34, "Wang, Ruopeng" mailto:rwa...@mgh.harvard.edu>> wrote: External Email - Use Caution What version of freesurfer are you using? I tried with 7.4.1 and the latest dev build, both can load these 2 files together without pr

Re: [Freesurfer] Use freeview to visualize white and pial surface

see if those work? What if you just bring up the pial and not the white? Maybe you can put those files in a dropbox and one of us (Ruopeng?) can take a look? From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.har

Re: [Freesurfer] freeview (visualize pial and white surface)

External Email - Use Caution Would it be possible to send us the two surface files? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of DS Sent: Thursday, August 3, 2023 3:30:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] f

Re: [Freesurfer] Freeview sudden termination

External Email - Use Caution .ctab is not an annotation file. Please try loading .annot files. Ruopeng On Aug 1, 2023, at 10:50 PM, Jacob Bunyamin mailto:jacob.bunya...@monash.edu>> wrote: External Email - Use Caution Hi, I am running freesurfer/7.3.2 and

Re: [Freesurfer] Freeview ERROR: label name '3rd-Ventricle' is duplicated (FSv6.0.0 with updated Freeview)

External Email - Use Caution Have you tried the latest Mac build of freeview? This has been fixed recently. On Jul 30, 2023, at 11:02 AM, Ha Manh Luu mailto:hal4...@med.cornell.edu>> wrote: External Email - Use Caution From: Ha Manh Luu Sent: Thursday, July 20, 2023

Re: [Freesurfer] Freesurfer Digest, Vol 232, Issue 12 - data not displayed

External Email - Use Caution Freeview requires OpenGL engine for fast editing (hardware accelerated hit test). So if you disable your graphics card, it is like not going to work. Maybe you need to update the graphics card driver to the latest? Ruopeng On Jun 23, 2023, at 1:27

Re: [Freesurfer] place pial matter on top of the cortex using segmentation volume

st useful information for me is at GM-pial boundary (the pink arrow)- for inflating, measuring curvature, or surface area or visualising the cortical thickneess. I hope this clarifies the problem. Thanks in advance. with regards, malav ____ From: "

Re: [Freesurfer] place pial matter on top of the cortex using segmentation volume

External Email - Use Caution I’m not sure if I understood what you are trying to show. If you want to show the cortical thickness on top of the pial surface, you can load it as an overlay. Ruopeng On Jun 14, 2023, at 7:30 AM, Malav Shah mailto:malav.s...@bccn-berlin.de

Re: [Freesurfer] freeview surface edgecolor overlay

/18RRIlfW8orAdONb8bSqGWriHwtoXhuC4U82129GHMM_ruuytXnN2a6KWWjlLZPYgJJgaLAPAebhHEwEu_enRieQsuAiHgjrI5TFZsd14HjyDNbjRBAyM-Aws2CLj3Qc-In25GKqI80tFV9ZKSvrKP41EjoO_0FpiAgX99Lr9RX60ZT1G9_XuvSCw4_-jtVNbsrstjnV2Cyp7B1dBgMPdkmKi9CgIiRD6zXUezj0PFPXt1ElXSg3AlcsfIitmFzODs15Dxo_ocqdHuKiUTxVhVQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview Ruopeng On May 5, 2023, at 3:54 AM, Dr. Cornelius

Re: [Freesurfer] freeview rh and lh overlay_mask files both showing in the lh hemisphere

External Email - Use Caution Would it be possible to send us the surface and the overlay and mask files so I can replicate the issue? Ruopeng On Apr 16, 2023, at 9:18 PM, Jewelia Karina Yao mailto:jewelia...@stanford.edu>> wrote: External Email - Use Cauti

Re: [Freesurfer] How to use custom fill with up to other labels flag

How about unchecking the “Up to unlabeled” option? On Apr 4, 2023, at 6:04 AM, Dilara Erişen mailto:dilara.eri...@gmail.com>> wrote: External Email - Use Caution Hi, I want to create ROI labels by dividing the activation cluster from functional localizer scan into visual areas. I use

Re: [Freesurfer] Freeview segmentation fault

segmentation fault External Email - Use Caution Hello, It was added to my ~/.bashrc file. Is this what you mean? Thank you, Ose On Tue, Apr 4, 2023 at 7:57 AM Wang, Ruopeng mailto:rwa...@mgh.harvard.edu>> wrote: Where is your license file located? On Apr 4, 2023, at 2:26 AM, OSE

Re: [Freesurfer] Freeview segmentation fault

Where is your license file located? On Apr 4, 2023, at 2:26 AM, OSE KADIRI mailto:osekad...@g.ucla.edu>> wrote: External Email - Use Caution Hello, I am having some trouble using Freeview on my university cluster with my MacBook (macOS Monterey version 12.4). Freeview works fine from

Re: [Freesurfer] automatic screenshots to all axial slices

You can do it from the menu File -> Save Movie Frames. Ruopeng On Mar 31, 2023, at 10:37 AM, Gonzalo Rojas Costa mailto:gonzalo.rojas.co...@gmail.com>> wrote: External Email - Use Caution Hi: I need to take screenshots of all axial slices of a volumetric image that I a

Re: [Freesurfer] FreeSurfer Segmentation Fault

esday, March 21, 2023 12:18 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault External Email - Use Caution Hi Ruopeng, This is the command I have been using: freeview tutorial_data_20190918_1558/diffusion_recon

Re: [Freesurfer] FreeSurfer Segmentation Fault

Can you post the full freeview command that you ran? Ruopeng On Mar 21, 2023, at 6:50 AM, Bartlett, Rob mailto:r.bartle...@exeter.ac.uk>> wrote: External Email - Use Caution Hi, I am using FreeSurfer 7.3.2 with Ubuntu 20.04.4 LTS. I have an issue where Freeview crashes

Re: [Freesurfer] Freeview Edit options restricted

Recon Edit mode will disable a few options. But it looks to me the Brush Size is not grayed out from your screenshot. To close the window, you can just switch to Navigate mode. Ruopeng On Mar 7, 2023, at 11:34 AM, Carlos Alcocer mailto:cd...@cornell.edu>> wrote: External Email

Re: [Freesurfer] Freeview displaying images in the wrong orientation

Freeview by default will display the image in its original pixel space, without re-sampling. You can try the -r flag to enable the resampling like this: freeview foo.mgz -r -cubic Ruopeng On Feb 27, 2023, at 7:04 AM, Nathan Kindred (PGR) mailto:n.kindr...@newcastle.ac.uk>>

Re: [Freesurfer] Freeview displaying images in the wrong orientation

Can you send us a screenshot or even better, a sample image file? Ruopeng > On Feb 22, 2023, at 7:34 AM, Nathan Kindred (PGR) > wrote: > >External Email - Use Caution > > Hi, > > When I am displaying certain images in freeview the orientation d

Re: [Freesurfer] neurological view on command line

I don’t think there’s a command line option for it. I’ll add it. Ruopeng From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Aaron Tanenbaum Sent: Wednesday, February 15, 2023 11:31:11 AM To: Freesurfer Subject: [Freesurfer] neurological view on command

Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

Can you try the latest dev build from here? https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Ruopeng On Feb 8, 2023, at 2:28 PM, Rankin McGugin mailto:rankin.mcgu...@gmail.com>> wrote: External Email - Use Caution of course, see attached Rankin W. McGugin, PhD Re

Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

Would it be possible to send us the full crash report? You can find it in the Console app. Best, Ruopeng On Feb 8, 2023, at 1:48 PM, Rankin McGugin mailto:rankin.mcgu...@gmail.com>> wrote: External Email - Use Caution Here is my error log: Last login: Wed Feb 8 12:03:23 on t

Re: [Freesurfer] Error:mghRead

Can you load the volume from menu File -> Load Volume? Ruopeng On Feb 2, 2023, at 2:21 PM, Lauren Stephens mailto:laure...@stanford.edu>> wrote: External Email - Use Caution Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behaviora

Re: [Freesurfer] Freeview label thickness: making the label outline thicker?

That edge thickness is for the intersecting outlines on the 2D slices. There is no settings for outline thickness for labels. Best, Ruopeng On Jan 8, 2023, at 10:58 AM, Greta Tuckute mailto:gret...@mit.edu>> wrote: Hi developers, I am using Freeview to plot overlays on inflated surface

Re: [Freesurfer] Freeview quit unexpectedly

After you load the image from the command-line, can you then load more images from the GUI? Ruopeng On Dec 20, 2022, at 3:23 AM, Addison, Reuben mailto:raddi...@mghihp.edu>> wrote: The answer to this is question ‘ opening an image from the gui ‘ is yes. The image only opens when I ope

Re: [Freesurfer] Use annotation for edgecolor in freeview

It should be the option to “Use overlay color”. But it appears the option does not work properly in the latest release. We will fix it asap. Ruopeng On Dec 16, 2022, at 6:43 AM, Chris Adamson mailto:chris.adam...@mcri.edu.au>> wrote: External Email - Use Caution Freesurfe

Re: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

You can run this command to clear the settings of freeview only: rm ~/.config/Massachusetts\ General\ Hospital/freeview.conf Ruopeng On Nov 15, 2022, at 5:05 PM, Dierker, Donna mailto:do...@wustl.edu>> wrote: External Email - Use Caution This happens to me when I control-C

Re: [Freesurfer] "Smooth display" in FreeView using command line

The flag is :smoothed=1. Ruopeng On Nov 4, 2022, at 11:43 AM, Arman Avesta mailto:avesta.ar...@yahoo.com>> wrote: External Email - Use Caution Hi Gang, Happy Friday! I'm using this little command to overlay two volumes (brainbox.mgz and target.nii.gz) in FreeView:

Re: [Freesurfer] Freesurfer labels vertices and not faces?

I’m not sure I get exactly what you wanted to do. But in freeview, surface colors are assigned by vertices, not faces. If the vertices of a face have different colors, the colors will be interpolated across the face by the rendering engine. If you turn on mesh display you will see that. On Nov

Re: [Freesurfer] overlay_threshold is ignored when using custom overlay

. Ruopeng On Oct 26, 2022, at 7:52 PM, Maya Yablonski mailto:ma...@stanford.edu>> wrote: External Email - Use Caution Hello, I'm trying to use a custom colormap for an overlay in Freeview and I can't get the threshold option to work. Specifically, I want to display posit

Re: [Freesurfer] Freeview: missing voxels in reconstructed surfaces

This appears to be a rendering artifact that happens sometimes with remote display. Are you viewing remotely from a Windows machine? Ruopeng On Oct 18, 2022, at 9:45 AM, Sarah Lavelle mailto:lavel...@tcd.ie>> wrote: External Email - Use Caution Dear Freesurfer, I have an issu

Re: [Freesurfer] Hemisphere in Yellow

Would it be possible to send me the overlay file? On Oct 7, 2022, at 1:27 PM, Jun Yeon Won mailto:wo...@umd.edu>> wrote: External Email - Use Caution Hi Ruopeng, I tried to adjust overlay thresholds in the Configure Overlay window, but I think it still looks weird. The gra

Re: [Freesurfer] Hemisphere in Yellow

You can adjust overlay thresholds in Configure Overlay window. Ruopeng On Oct 6, 2022, at 10:49 AM, Jun Yeon Won mailto:wo...@umd.edu>> wrote: External Email - Use Caution Dear Freesurfer experts, I am running a linear regression analysis and found a significant result s

Re: [Freesurfer] Freeview does not show images

Are you able to run glxgears command? Do you see spinning gears? Ruopeng On Oct 6, 2022, at 4:28 AM, Justina Lee mailto:justinale...@gmail.com>> wrote: External Email - Use Caution To whom this may concern and can help, I am currently trying to run Freeview under the W

Re: [Freesurfer] Freeview Closes Unexpectedly

e file? On Fri, Jul 22, 2022 at 1:31 AM Wang, Ruopeng mailto:rwa...@mgh.harvard.edu>> wrote: Have you install the FS license file properly? Another thing to check is to make sure you have granted freeview permission to access your disk files. You can check it in the system preferences.

Re: [Freesurfer] Freeview Closes Unexpectedly

Have you install the FS license file properly? Another thing to check is to make sure you have granted freeview permission to access your disk files. You can check it in the system preferences. Ruopeng On Jul 21, 2022, at 12:31 PM, user2038...@gmail.com<mailto:user2038...@gmail.com>

Re: [Freesurfer] Standalone freeview

There is only a stand-alone version for macOS. You can download it from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview You’ll still need to install a license file properly. Best, Ruopeng > On Jul 5, 2022, at 5:19 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) >

Re: [Freesurfer] Freeview XDG_runtime_dir not set

This thread might be helpful: https://stackoverflow.com/questions/59790350/qstandardpaths-xdg-runtime-dir-not-set-defaulting-to-tmp-runtime-aadithyasb Ruopeng On Jun 5, 2022, at 9:29 PM, Manuela Dorado Novoa mailto:manue...@uw.edu>> wrote: External Email - Use Caution Hi Free

Re: [Freesurfer] Orthographic camera in FreeView

Hi Anderson, I’ve added “Orthographic view” option for the 3D viewport. It can be activated from right click menu in the view. You can download the latest build of freeview here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On Apr 15, 2022, at 10:23 AM, Anderson M

Re: [Freesurfer] Advice: changing Freeview light source?

/UpdateFreeview Best, Ruopeng On Mar 28, 2022, at 6:45 PM, Sam Buck Johnson mailto:samjo...@stanford.edu>> wrote: External Email - Use Caution Dear Freesurfer Community, I use Freeview to render 3D views of overlays on cortical surfaces. For my current processing, the absolute scale

Re: [Freesurfer] transitioning from tkmedit to freeview

e left click now) There is an option under Tools -> Preferences -> Special Settings -> Edit to allow right click to erase a voxel. Best, Ruopeng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

Re: [Freesurfer] bug: freeview's "configure overlay" window frozen (Ubuntu18 in wsl2 on Windows 11)

Can you try MobaXterm instead of xming: https://mobaxterm.mobatek.net/ On Mar 16, 2022, at 12:21 PM, Sebastien Proulx wrote: External Email - Use Caution Update: -I tried reinstalling Xming, precisely following these instructions

Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: Freeview error on centos7

I had no problem loading these files. Maybe it’s the surface file? Can you also send the surface file? On Mar 14, 2022, at 8:20 PM, Wen Wen mailto:wenw2...@gmail.com>> wrote: External Email - Use Caution Hi Ruopeng, Thank you for your reply. Please see attached. Visualizing pr

Re: [Freesurfer] Custom Freeview Color Map (not Lookup Table)

The stock colormaps are hard-coded. I can add an option to load custom color map. On Mar 14, 2022, at 11:58 AM, Keator, David (Psychiatry & Human Behavior) mailto:dbkea...@hs.uci.edu>> wrote: External Email - Use Caution Hi Ruopeng, I have the colormap I’m interested in us

Re: [Freesurfer] Freeview error on centos7

Would it be possible to send us the volume and the surface files so that we can try to replicate the issue? Thanks, Ruopeng On Mar 14, 2022, at 12:01 PM, Wen Wen mailto:wenw2...@gmail.com>> wrote: External Email - Use Caution Dear Freesurfer experts, I’m running Freevie

Re: [Freesurfer] Custom Freeview Color Map (not Lookup Table)

There isn’t a way to do that at the moment. So you want to use a continuous spectrum with 256 color stops as the color map? Ruopeng On Mar 11, 2022, at 6:06 PM, Keator, David (Psychiatry & Human Behavior) mailto:dbkea...@hs.uci.edu>> wrote: External Email - Use Caution Hi,

Re: [Freesurfer] Advice? Re: Freeview 7.1.1 won't start on Mac: segmentation fault

You can also download the latest build of freeview here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Ruopeng On Mar 1, 2022, at 7:44 PM, Adam Martersteck mailto:acmar...@gmail.com>> wrote: External Email - Use Caution Hi Sam, I can tell from your crash report yo

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

A%2F%2Fwww.uq.edu.au%2F> From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Wang, Ruopeng mailto:rwa...@mgh.harvard.edu>> Sent: Friday

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

Re: [Freesurfer] QXcbConnection

-UwwpJFVGd8JPRGPHhY5Fl-yxajETe8sSnoSMBnr5ZmWvNaUl1wh76TWCEorIawgV6N4LAZLGsTBVAV0GCNax3Tt-PGw9Y8HOF46nrV0wo6rA/https%3A%2F%2Fmobaxterm.mobatek.net%2F Best, Ruopeng On Dec 30, 2021, at 7:51 AM, Carina Forster mailto:carinaforster0...@gmail.com>> wrote: External Email - Use Caution Dear Free

Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations

What version of Freesurfer are you using? Would it be possible to send us the volume files before and after the rotation? Best, Ruopeng On Dec 14, 2021, at 6:10 PM, Christopher Panks mailto:cpa...@uw.edu>> wrote: External Email - Use Caution I’m trying to get images of post-

Re: [Freesurfer] Inflated surfaces on FS7 looking different

From the screenshot it looks like a remote display issue. Maybe you can try a different X client, such as MobaXterm (https://mobaxterm.mobatek.net) ? Ruopeng On Oct 29, 2021, at 5:54 AM, DIANA ORTEGA CRUZ <100315...@alumnos.uc3m.es<mailto:100315...@alumnos.uc3m.es>> wrote:

Re: [Freesurfer] Customising overlay

What version of freesurfer are you using? I tried the latest freeview build and had no problem inserting colors at arbitrary value for customized color option. Best, Ruopeng On Sep 23, 2021, at 9:00 AM, Worker, Amanda mailto:amanda.wor...@kcl.ac.uk>> wrote: External Email

Re: [Freesurfer] running freeview on MacOS Big Sur, version 11.5.2

I assume you’ve granted freeview permission to access files on your local drive? On Sep 14, 2021, at 3:17 PM, Jingyi Wang mailto:jy_w...@ucsb.edu>> wrote: External Email - Use Caution Hello Ruopeng, Thank you for your reply. Yes, my freeview can open. But whenever I open any

Re: [Freesurfer] running freeview on MacOS Big Sur, version 11.5.2

Would freeview start up without loading a volume? Ruopeng On Sep 14, 2021, at 12:48 PM, Jingyi Wang mailto:jy_w...@ucsb.edu>> wrote: External Email - Use Caution Dear freesurfer experts, I have a MacOS Big Sur, version 11.5.2 with an Intel chip. I successfully installed free

Re: [Freesurfer] Issue with opening freeview

Can you click on Show Details button and send us the whole crash report in the box? Ruopeng On Sep 7, 2021, at 10:30 AM, Eunbi Kwon mailto:eunbi.k...@northwestern.edu>> wrote: External Email - Use Caution Hello, I'm using freeview version 7.2.2 on my macOS Catalina (vers

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Would it be possible to send me the dicom files? Ruopeng On Sep 1, 2021, at 1:14 PM, Peled, Noam mailto:npe...@mgh.harvard.edu>> wrote: The same error. Also, when trying to run recon-all on these files. Thanks, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesu

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

What if you use mri_convert to convert them to a mgz or nii volume? Do you get the same error? Ruopeng On Sep 1, 2021, at 10:52 AM, Peled, Noam mailto:npe...@mgh.harvard.edu>> wrote: Hello! I’m trying to use freeview to visualize FSPGR dicoms files. I’m using ubuntu 18.04 with tcsh

Re: [Freesurfer] See masked area in freeview

That is not an annotation file. Try the one with .annot suffix. Ruopeng On Aug 31, 2021, at 12:07 PM, Haley Park mailto:hpar...@gmail.com>> wrote: External Email - Use Caution Thank you! When I tried that I get a series of error messages like this: MRISreadAnnotationInt

Re: [Freesurfer] See masked area in freeview

You can load them as annotations in freeview along with your overlay. Change the z-order of the overlay to be larger than the annotation so that the overlay will be displayed on top of the annotation. Ruopeng On Aug 31, 2021, at 10:16 AM, Haley Park mailto:hpar...@gmail.com>>

Re: [Freesurfer] [Quick Question] Freeview Update

For editing it should be safe to update freeview. Ruopeng On Aug 12, 2021, at 3:20 PM, Boa Sorte Silva, Narlon mailto:narlon.si...@ubc.ca>> wrote: External Email - Use Caution Dear FreeSurfer team, We have half of our sample edited in Freeview V2, we wanted to updated to the

Re: [Freesurfer] Freeview question

Hi Mona, The neg.label file has all negative scalar values in it, where the default threshold for the label is set to 0. If you set the threshold to a big negative number it will show up. Best, Ruopeng On Jul 22, 2021, at 3:35 PM, Nasiriavanaki, Zahra,M.D. mailto:znasiriavan

Re: [Freesurfer] FreeView issue!

Can you try resetting freeview’s preferences. You can do it in a terminal with the following command: rm ~/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plist Wait for a few seconds and try starting freeview again. Ruopeng On Jul 21, 2021, at 1:49 PM, Sahil Bajaj mailto:sahil.br

Re: [Freesurfer] FreeView issue!

What if you run: $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview -f fsaverage/surf/lh.inflated > On Jul 16, 2021, at 1:07 PM, Sahil Bajaj wrote: > > External Email - Use Caution > > > Hi everyone, > > I am having following error while opening freeview in terminal: > >

Re: [Freesurfer] Mac OS problem with .pial files

On Big Sur you will need to grant permissions to read and write for all the freesurfer binaries. Have you done so? Also, you can download the latest standalone build of freeview for macOS here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Ruopeng On Jul 16, 2021, at 10:13 AM

Re: [Freesurfer] Freeview filled in labels along with their outlines

It is possible to show outline only but not combined with filled ones. Ruopeng On Jul 8, 2021, at 5:02 PM, Pradyumna Bharadwaj mailto:p...@email.arizona.edu>> wrote: External Email - Use Caution Hi, In freeview, is it possible to view a collection of labels with different fil

Re: [Freesurfer] Masking A Surface Overlay

You can click on “Configure Overlay” button on the left pane to adjust threshold for the overlay display. Ruopeng On Jun 29, 2021, at 9:53 AM, Jacoby, John mailto:jjac...@mgh.harvard.edu>> wrote: Hi all, I've used mri_glmfit to run some GLMs on surface data. Now I would like to

Re: [Freesurfer] Changing script from tksurfer to freeview

Would it be possible for you to try FS 7.1 or the dev version? Freeview has evolved greatly since 6.0 with a lot of added functionalities. There is also a script called tksurferfv that runs freeview with arguments like tksurfer. Ruopeng On Jun 25, 2021, at 12:58 PM, Marlene Staginnus

Re: [Freesurfer] Saving ROIs on freeview

Can you try the latest build of freeview for macOS? You can download it from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Ruopeng On Jun 24, 2021, at 6:09 PM, Tina Thomas mailto:tinathoma...@gmail.com>> wrote: External Email - Use Caution Hello, I am atte

Re: [Freesurfer] how to visualize statistical maps in FS7.1?

After you load the overlay onto the surface, you can click on “Configure Overlay” button on the left pane to adjust color scale and thresholds for the overlay. Ruopeng > On Jun 11, 2021, at 11:53 AM, Bernardoni, Fabio > wrote: > >External Email - Use Caution &

Re: [Freesurfer] blurring average label files

Hi Kristi, I think the color scale bar only sync with overlays, not labels. I will change that. Best Ruopeng On May 20, 2021, at 3:22 PM, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> wrote: I defer to Ruopeng for the 2nd question. And for the first Doug knows the exact formula to g

Re: [Freesurfer] Freeview Update using MAC

Email - Use Caution External Email - Use Caution Hi Ruopeng, Thank you for the quick reply. When I attempt to untar Freeview: erikanolan$ tar -xzvf /Users/erikanolan/Downloads/freesurfer-darwin-macOS-HighSierra-dev-freeview.tar.gz tar: Error opening archive: Failed to open '/

Re: [Freesurfer] Freeview Update using MAC

Hi Erika, What error message do you get when you launch Freeview on your macOS 10.12? Ruopeng On May 18, 2021, at 1:57 PM, Erika Nolan mailto:erika.no...@mail.mcgill.ca>> wrote: External Email - Use Caution External Email - Use Caution Good afternoon, I down

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

Thanks for the file. Did the user experience slow-down while generating the profile (other than the slow-down by valgrind)? Ruopeng On May 5, 2021, at 7:40 AM, Torkil Svensgaard mailto:tor...@drcmr.dk>> wrote: External Email - Use Caution Hi Ruopeng All the boxes are fully up

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

Load a couple of volumes and/or surfaces, play with it a little bit and close it. There should be a file called callgrind.out. generated by valgrind. Can you send us the file? Thanks, Ruopeng On May 4, 2021, at 2:44 AM, Torkil Svensgaard mailto:tor...@drcmr.dk>> wrote: Ex

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

went away. Ruopeng On May 4, 2021, at 2:44 AM, Torkil Svensgaard mailto:tor...@drcmr.dk>> wrote: External Email - Use Caution Hi again Also the same when run via X11 from a beastly compute node. As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we ar

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display? Ruopeng > On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard wrote: > >External Email - Use Caution > > Hi again > > The user r

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

Hi Torkil, Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest? Best, Ruopeng > On Apr 26, 2021, at 6:06 AM, Torkil Svensga

Re: [Freesurfer] Freeview issues with surfaces

There is a ‘Overlay’ drop down box on the left pane, where you can load overlay after loading a surface. Ruopeng On Apr 26, 2021, at 9:49 AM, Pål Gunnar Larsson mailto:p...@ous-hf.no>> wrote: External Email - Use Caution Thank you. In version 5 I could load an overlay wi

Re: [Freesurfer] Freeview issues with surfaces

Hi Pål, lh.area and lh.thickness are not surface files. They can be loaded as a surface overlay like this: freeview -f lh.pial:overlay=lh.thickness Best, Ruopeng On Apr 26, 2021, at 9:36 AM, Pål Gunnar Larsson mailto:p...@ous-hf.no>> wrote: External Email - Use Caution I hav

Re: [Freesurfer] tksurfer question

Hi, Tksurfer has been replaced by freeview. You can load an overlay file with the following freeview command: freeview -f lh.inflated:overlay=xxx.mgh Best, Ruopeng On Mar 1, 2021, at 2:32 PM, DS mailto:zky...@126.com>> wrote: External Email - Use Caution Dear experts, I want

Re: [Freesurfer] Freeview cmmd + F

I don’t think older version has it. Ruopeng On Feb 25, 2021, at 3:49 PM, Boa Sorte Silva, Narlon mailto:narlon.si...@ubc.ca>> wrote: External Email - Use Caution Hi all, For FreeView version 1 for Mac is there a similar command that can be used to toggle all surfaces, simi

Re: [Freesurfer] Drawing labels on flat patch.

the flat patch directly. Best, Ruopeng On Feb 21, 2021, at 12:06 AM, Devavrat Vartak mailto:dvar...@berkeley.edu>> wrote: External Email - Use Caution Hello freesurfer experts, Freeview v3.0 FS 7.1.1 I am able to draw labels on the 3D surface and display it on a flat patch, but

Re: [Freesurfer] FreeSurfer 7 vs FreeSurfer 6 surface differences

FYI, translucent surfaces in freeview do not render properly due to the limitation of old VTK libs being used. I would not use it for error checking in this case. Ruopeng On Feb 16, 2021, at 11:55 AM, Mike Schmidt mailto:mikeschm...@schmidtgracen.com>> wrote: External Email

Re: [Freesurfer] define freeview colormap from command line

You can specify custom colors like this: freeview -f lh.inlfated:overlay=xxx:overlay_custom=val,r,g,b,val2,r2,g2,b2 ... val is the value of the color point, r, g, b are RGB values in the range of 0 to 255. You can find more details from ‘freeview -h’. Best, Ruopeng > On Feb 3, 2021, at 6

Re: [Freesurfer] Saving more than one figure using freeview

For command file you don’t need to add -noquit. On Jan 27, 2021, at 10:28 AM, Peled, Noam mailto:npe...@mgh.harvard.edu>> wrote: That’s great! Thanks Ruopeng! Should I also add the -noquit flag in each line: freeview foo.mgz -viewport x -ss pic1.jpg -noquit -viewport y -ss pic2.jpg -

Re: [Freesurfer] Saving more than one figure using freeview

-ss pic3.jpg Then run: freeview -cmd foo.txt Ruopeng On Jan 26, 2021, at 1:18 PM, Peled, Noam mailto:npe...@mgh.harvard.edu>> wrote: Hello all, Can I use the -ss flag in freeview to save more than one figure? Currently, I’m calling freeiew 3 times, each time with a different viewport (sa

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