Re: [Freesurfer] freeview command for displaying selected labels

Hi Rene, I don’t think you can do it from the command-line. We’ll add an option for it. Best, Ruopeng > On May 29, 2020, at 10:15 AM, Schranzer René > wrote: > > External Email - Use Caution > > > Hello FreeSurfer Developers, > > is there a way to display only selected

Re: [Freesurfer] freeview is RAM greedy in version 7.1.0

> Komu: > Kopie: > Odesláno: 23.5.2020 3:03 > Předmět: Re: [Freesurfer] freeview is RAM greedy in version 7.1.0 > > Please also let us know the version of the OS you are comparing running both > the 6.0.0 and 7.1.0 release on. > > - R. > >> On May 22, 2020, at

Re: [Freesurfer] freeview is RAM greedy in version 7.1.0

Hi Antonin, Thanks for the report. We’ll look into this. Best, Ruopeng > On May 22, 2020, at 2:42 PM, Antonín Škoch wrote: > > External Email - Use Caution > > > Dear experts, > > I want to use freeview for viewing Gordon surface labels on inflated surface > with custom

Re: [Freesurfer] [External] Re: Freesurfer display resolution very low compared to other viewers

uch thanks all! > > BR > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Ruopeng Wang > > Sent: Tuesday, April 14, 2020 11:10 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution very > low compared to other

Re: [Freesurfer] [External] Re: Freesurfer display resolution very low compared to other viewers

Hi Brian, Can you load a single volume in freeview to compare? Maybe also use similar window/level? The one in the picture appears smoothed to me (may due to trilinear sampling if it is not the first loaded volume). Best, Ruopeng > On Apr 14, 2020, at 1:14 PM, Renner, Brian wrote: > >

Re: [Freesurfer] Fwd: Is it possible to load flatmaps in freeview and draw ROI's on them?

Hi Devavrat, Freeview in FS 6.0 can’t load patches but the upcoming FS 7 can. If you want to give it try, you can download the latest build from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview To load a patch, run:

Re: [Freesurfer] (no subject)

ason to not display negative scales with look up > table? Will it cause any error or jeopardize the results displayed? > > Many Thanks > > Peng > > > On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang <mailto:rpw...@nmr.mgh.harvard.edu>> wrote: > Hi Peng, > > Your

Re: [Freesurfer] (no subject)

Hi Peng, Your lookup table only contains indices between 0 to 6. In any case I would not use look up table to display negative scales. Have you tried any other color maps like JET or NIH which has more colors? Best, Ruopeng > On Apr 6, 2020, at 6:30 AM, Peng Liu wrote: > > External

Re: [Freesurfer] Tkmedit gui download

Hi Victor, I don’t think you can download standalone tkmedit. But you can download standalone freeview for your Mac from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview FYI, tkmedit has been depreciated. You try

Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations

You can go to menu Tools -> Transform Volume to adjust the registration and save it as a lta registration file. Then run lta_convert to convert it to xfm: lta_convert --inlta foo.lta --outmni foo.xfm > On Mar 31, 2020, at 1:06 PM, Rachel Hoel > wrote: > >

Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations

Hi Rachel, You need to enter the full path of the transformation file or relative one like /mri/... Best, Ruopeng > On Mar 31, 2020, at 12:20 AM, Rachel Hoel wrote: > > External Email - Use Caution > Dear Freesurfer Developers, > > I'm working with v6.0 on OS Catalina 10.15

Re: [Freesurfer] Freeview CLI feature request

Sure. We’ll add those in. Best, Ruopeng > On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS > wrote: > > External Email - Use Caution > > > Dear FreeSurfer team, > > I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39 > > Would it be possible to add the

Re: [Freesurfer] overlay threshold in freeview

ers after comma? > > Thank you again! > > >> Il giorno 10 mar 2020, alle ore 16:44, Ruopeng Wang >> mailto:rpw...@nmr.mgh.harvard.edu>> ha scritto: >> >> HI Rachele, >> >> You can set overlay threshold from the command-line like this: >

Re: [Freesurfer] overlay threshold in freeview

HI Rachele, You can set overlay threshold from the command-line like this: freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=low,high More information about threshold setting can be found by: freeview -h Best, Ruopeng On 3/10/20 11:29 AM, Rachele Sanfelici wrote:

Re: [Freesurfer] freeview failed to load Surface overlay

Hi Meike, Would it be possible to send us one of the sig.mgh files to inspect? Thanks, Ruopeng On 3/9/20 3:24 PM, Meike Hettwer wrote: External Email - Use Caution Dear freesurfer experts, I am currently running a very basic correlation with two groups (gender, which I am not

Re: [Freesurfer] Cannot load overlay through GUI

Hi Fengdan, Can try the latest development build of freeview? It should work better on newer macOS. You can get it from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 1/29/20 5:20 PM, Fengdan Ye wrote: > External Email - Use Caution > > Dear

Re: [Freesurfer] Freeview froze when trying to open volume file

You probably need to grant freeview permission to access your files and folders if you have not. You can check in System Preferences. Ruopeng On 1/23/20 2:16 PM, Tarui, Tomo wrote: External Email - Use Caution Dear Freesurfer community, I have been also experiencing problem that

Re: [Freesurfer] Freeview Surface Loading View Center

Hi Alex, If the there is volume geometry information in the surface header, freeview will display the surface in that coordinate. Otherwise it will display it in surfaceRAS. The center of the view is automatically set as the center of FOV of the surface. Best, Ruopeng > On Jan 19, 2020, at

Re: [Freesurfer] Freeview - command-line label sub-option "opacity" does not work

gt; I see now, that the reason of my problem is that the "opacity" flag is > dedicated for volume labels (loaded by -l flag), not surface labels (loaded > by sub-option :label=label_file ) isn't it? > > Is it possible to control opacity of surface labels? > > Anton

Re: [Freesurfer] Freeview - command-line label sub-option "opacity" does not work

Can you post the full command? Ruopeng > On Dec 30, 2019, at 1:10 PM, Antonin Skoch wrote: > >  > External Email - Use Caution > > Dear experts, > > a freeview command-line label sub-option "opacity" does not work for me. > > Freeview exits with error: Unrecognized

Re: [Freesurfer] Save output as attach file

surfer > V6. > Can i do this procedure to update freeview on it or i must install v6. > Best regards and best wishes. > Nader > > > On Tue, 24 Dec 2019, 19:09 Ruopeng Wang <mailto:rpw...@nmr.mgh.harvard.edu> wrote: > Hi Nadar, > > I’ve added a new volume filter c

Re: [Freesurfer] Save output as attach file

s and best wishes > Nader > > On 23 Dec 2019 19:24, "Ruopeng Wang" <mailto:rpw...@nmr.mgh.harvard.edu>> wrote: > Hi Nader, > > Freeview can't do that currently. But I will add an option for it. > > Best, > Ruopeng > > > On 12/21/19 10:19

Re: [Freesurfer] Save output as attach file

Hi Nader, Freeview can't do that currently. But I will add an option for it. Best, Ruopeng On 12/21/19 10:19 AM, Bruce Fischl wrote: > oh, you want to save a volume that has just the borders of each > structure labeled? I'm not sure we have anything that can do that. > Ruopeng: can freeview?

Re: [Freesurfer] Trouble running Freeview from Mac Terminal

Hi Jason, Can you try this command in a terminal on your Mac: defaults write org.macosforge.xquartz.X11 enable_iglx -bool true Then make sure to restart XQuartz and ssh -X to your linux box. It works for me on macOS 10.12. Ruopeng On 12/4/19 10:59 AM, Stockmann, Jason wrote: Hi, I have

Re: [Freesurfer] V1 length

Hi Melissa, You can now measure the length of a path on surfaces in the development version of freeview. You can download the dev build here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview On the surface panel, click on "Path/Custom Fill" icon and draw the path. Then hold the

Re: [Freesurfer] freeview: load multiple volumes with a single option

Hi Ikbeom, I think this is because the added options at the end of file path are treated as part of the path by the shell and thus returns no match. I will try to put a fix on that. Best, Ruopeng On 10/16/19 4:09 PM, Jang, Ikbeom wrote: Dear FreeSurfer community: I am a beginner and

Re: [Freesurfer] freeview command line options

Hi Eli, The bug has been fixed. You can follow these steps to update freeview to the latest dev build: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 9/20/19 4:14 PM, Rockers, Elijah D. wrote: External Email - Use Caution Hello, it's possible I

Re: [Freesurfer] freeview command line options

Hi Eli, I can confirm this is a bug. We'll fix it very soon. Best, Ruopeng On 9/20/19 4:14 PM, Rockers, Elijah D. wrote: External Email - Use Caution Hello, it's possible I found a bug in freeview: I'm using the overlay_color option with freeview. Specifically I am trying to

Re: [Freesurfer] Freeview error

/brainmask.mgz /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang (mailto:rpw...@nmr.mgh.harvard.edu>>) escribió: Can you run the command in the command window that you start freeview? Ruopeng On Sep 16, 2019, at 5

Re: [Freesurfer] Freeview error

he freeview command console and this is the output > > [FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz > This is not a shell. Only freeview commands are supported. Type '-h' for all > the available commands. > > > > Best regards, > > El lu

Re: [Freesurfer] 001 vs brainmask views in freeview

...@nmr.mgh.harvard.edu *On Behalf Of *Ruopeng Wang *Sent:* Monday, September 16, 2019 1:17 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] 001 vs brainmask views in freeview The first volume is always displayed in its original orientation where pixel data are stored. So

Re: [Freesurfer] 001 vs brainmask views in freeview

Of *Ruopeng Wang *Sent:* Monday, September 16, 2019 11:51 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] 001 vs brainmask views in freeview Hi, When you load brainmask.mgz as the second volume, it will be realigned to 001.mgz. The default resample method is nearest-neighbor. Thus you

Re: [Freesurfer] 001 vs brainmask views in freeview

Hi, When you load brainmask.mgz as the second volume, it will be realigned to 001.mgz. The default resample method is nearest-neighbor. Thus you get the blocky look. You can try loading it with trilinear or cubic resampling like this from the command-line: freeview -v 001.mgz brainmask.mgz

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

The scalar bar display for overlay in stable 6.0 is broken. If you can install the latest dev build, you should be able to see the scalar bar: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 9/11/19 9:57 AM, Caspar M. Schwiedrzik wrote: External Email - Use

Re: [Freesurfer] freeview crash -- petsc error when opening volume

else I can do to help troubleshoot? Tristan *From:*freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ruopeng Wang *Sent:*Thursday, August 22, 2019 5:00 PM *To:*Freesurfer support list *Subject:*Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tris

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

Hi Caspar, In freeview, once you load a overlay onto a surface, you can click on "Configure" button under "overlay" settings on the panel to adjust overlay display. There is a colorwheel option in it. From command-line, it can be activated like this: freeview -f

Re: [Freesurfer] FreeView : Tools : Volume Filter : Close

Hi Ysr, I think it just uses a 3x3x3 kernel. Best, Ruopeng On 9/4/19 10:51 AM, Yasir Hadi wrote: External Email - Use Caution Hello FreeSurfer Developers, I just want to get the Information: which parameters are used as I apply the filter *Close* on the volume dataset using the

Re: [Freesurfer] viewport does not affect snapshots for --slice option in cmd mode

8 -0.9976 -0.0515 131.6617 > -0.0119 0.0510 -0.9986 148.0342 >-0.9988 -0.0474 0.009596.2251 >-0. -0. -0. 1. > > On Thu, Aug 29, 2019 at 9:55 AM Ruopeng Wang <mailto:rpw...@nmr.mgh.harvard

Re: [Freesurfer] viewport does not affect snapshots for --slice option in cmd mode

Hi Harris, The slice option tales arguments as the original col, row and slice. So they are not necessarily in Sagittal, coronal and axial order, depending on the original orientation of the volume. If you run mri_info on the volume, what does the orientation show? Best, Ruopeng > On Aug

Re: [Freesurfer] trouble with freeview View > Show Color Scale

Hi Liz, Would it be possible to send me the data file so I can give it a try? Best, Ruopeng > On Aug 23, 2019, at 1:12 PM, Elizabeth Olson wrote: > > External Email - Use Caution > > > Hello, > > I'm having a bit of trouble with the Show Color Scale option. I have run >

Re: [Freesurfer] freeview crash -- petsc error when opening volume

s sequentially through the GUI. > > Thank you! > Tristan > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Ruopeng Wang > > Sent: Thursday, August 22, 2019 8:16 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] freeview crash -- petsc error

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan, Would it be possible to send us the files and the command-line you run? Best, Ruopeng > On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH wrote: > > External Email - Use Caution > Adding more details provided by my user: > > The crash only happens when loading

Re: [Freesurfer] spatial scale bar question

13th Street, 149-2615 > Charlestown, MA, USA, 02129 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Ruopeng Wang > > Sent: Friday, August 16, 2019 8:46:57 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] spatial scale bar question > >

Re: [Freesurfer] spatial scale bar question

Hi Mona, If you are running the latest dev build, you can right click in the 3D view and choose “Show 3D scale”. The scale bars can only be placed at the boundary of the FOV. Best, Ruopeng > On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra > wrote: > > Hi Freesurfer experts > > I wanted

Re: [Freesurfer] Error opening Freeview

Hi Victor, Would it be possible to send me the data files and the freeview command you ran? You can upload them from here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks, Ruopeng On 7/1/19 4:29 PM, Zeng,Victor (BIDMC - Psychiatry) wrote: ​Hi all, I'm having issues opening

Re: [Freesurfer] TrackVis question

You need to use the gradients extracted from the data by FSL (or freesurfer). Ruopeng > On May 23, 2019, at 5:02 PM, Alan Francis wrote: > > External Email - Use Caution > > > Hi Ruopeng - > > I used Diffusion Toolkit to recon DTI data that was preprocessed using FSL. >

Re: [Freesurfer] Fwd: Visualizing Volumetric Files on Surface

Hi Maedeh, I'm not quite clear about what exactly you want to do but have you tried loading the volume as an overlay to the surface in freeview? Best, Ruopeng On 5/9/19 12:47 PM, Maedeh Khalilian wrote: > External Email - Use Caution > >> From: "Maedeh Khalilian" >> To:

Re: [Freesurfer] Color scale error

Can you try turning off/on the scale bar or change the threshold a little bit and see if it updates? Ruopeng > On May 1, 2019, at 2:48 PM, Nillo, Ryan Michael R > wrote: > > External Email - Use Caution > > > Hello FreeSurfer Developers. > > I am using FSv6 and I am having

Re: [Freesurfer] freeview and complex values

Hi Shahin, Freeview does not support color wheel colormap yet. We will add that option very soon. Best, Ruopeng On 4/22/19 2:52 PM, sha...@nmr.mgh.harvard.edu wrote: > Hi Surfers, > I am trying to use freeview to present retinotopy mapping in > subcortical regions. I need to show complex

Re: [Freesurfer] Custom Colormap

Hi Emanuel, You can use this command to load customized color table file: freeview -v brain.mgz:colormap=lut:lut=color_table_file.txt Best, Ruopeng On 4/1/19 10:40 AM, Emanuel Alvaredo wrote: Thanks Bruce, Do you know what is the command line option? Thanks! Emanuel On Mon, Apr 1, 2019 at

Re: [Freesurfer] [how to highlight a known ROI in original MR Image]

se? > > Best Regards, > Yi > > On 20 Mar 2019, at 3:44 PM, Ruopeng Wang wrote: > >> Hi Yi, >> >> If you update to the latest development build of freeview, you can display a >> single label or any number of selected labels in aseg. Here is how to upda

Re: [Freesurfer] [how to highlight a known ROI in original MR Image]

Hi Yi, If you update to the latest development build of freeview, you can display a single label or any number of selected labels in aseg. Here is how to update your freeview: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 3/20/19 3:20 PM, Yi Li wrote:

Re: [Freesurfer] problems with Freeview

You can send via filedrop here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Use rpwang as recipient. Thanks. On 1/31/19 11:29 AM, Laboratorio de Neurociencia Funcional wrote: Please let me know how to send you these files. El jue., 31 ene. 2019 a las 17:19, Ruopeng Wang (mailto:rpw

Re: [Freesurfer] problems with Freeview

arises when we display FS images with Freeview using Freesurfer (6.0 or development version). For that reason, I asked you about issues installing Freeview, or wrong interaction between Ubuntu and Freeview. Any suggestion? El jue., 31 ene. 2019 a las 16:30, Ruopeng Wang (mailto:rpw

Re: [Freesurfer] problems with Freeview

datasets and the > problem persists. Could the problem be related to the way that we have > installed Freeview or something wrong between Freeview and the Ubuntu version > that we are using (16.04 TLS)? > > Best, > Jose > > El jue., 31 ene. 2019 a las 15:32, Ruopeng Wa

Re: [Freesurfer] problems with Freeview

0/surf/rh.pial:edgecolor=red > > Looking forward your comments. > > Best, Jose > > > El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang ( <mailto:rpw...@nmr.mgh.harvard.edu>>) escribió: > Can you share the freeview command you run to load the these data? > >

Re: [Freesurfer] problems with Freeview

Can you share the freeview command you run to load the these data? Ruopeng > On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional > wrote: > > External Email - Use Caution > > > Dear Freesurfers, > > we have installed the updated Freeview version in the

Re: [Freesurfer] Highlighting single atlas structures in freeview

HI Francesco, The latest development version of freeview can do this. You can download it from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng > On Jan 21, 2019, at 8:54 AM, Francesco Puccettone >

Re: [Freesurfer] (no subject)

Hi Larissa, The latest development version of freeview supports drawing labels on surface. You can take a look here on how to update freeview: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview In the latest version, you can draw paths on surface and use custom fill to create/edit

Re: [Freesurfer] Freeview Scrolling through slices on a Mac

What version of freesurfer are you running? I think in 6.0, up/down arrow keys will scroll through slices. If not, the latest dev build should have it. You can get the latest freeview build here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 12/11/2018 01:23 PM,

Re: [Freesurfer] freeview showing results in a strange manner

What is your freeview command? Is there any message shown in the terminal? Ruopeng > On Nov 21, 2018, at 5:07 PM, 姜时泽 wrote: > > Dear freesurfer experts, > I am using freesurfer to analyze my PET data according to the tutorial > online. It works pretty well and I write the values of the

Re: [Freesurfer] automating custom color map

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ruopeng Wang *Sent:* Thursday, November 1, 2018 7:18:34 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] automating custom color map I think there is no option to set

Re: [Freesurfer] automating custom color map

I think there is no option to set custom color code for overlay from command-line. I’ll add that option and let you know when it’s ready. Best, Ruopeng > On Nov 1, 2018, at 4:51 PM, Nillo, Ryan Michael R > wrote: > > External Email - Use Caution > Hi Freesurfer Users, > > I

Re: [Freesurfer] Freeview coordinates

Hi Florent, I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 73, 1), you should get -24, -55, 62 Which matches what is shown in freeview. Best, Ruopeng On 10/26/2018 12:06 PM, k3...@free.fr wrote: External Email - Use Caution Hi Bruce, Thanks for

Re: [Freesurfer] Freeview: Load multiples overlays for one surface

Yes, it is possible. But you should use ':' as separator like this: -f surf/lh.inflated:overlay=surf/lh.sulc:overlay=surf/lh.thickness:overlay_threshold=1,5 Ruopeng On 09/07/2018 03:11 PM, Emanuel Alvaredo wrote: External Email - Use Caution Hi! I would like from command line to

Re: [Freesurfer] Did not find any volume info. Warning: MatrixInverse failed

Were they loaded with the same command? Can you check freeview's build time to make sure they are the same build? You can check it from menu Help->About. Ruopeng On 09/06/2018 09:15 AM, Sofia Rodriguez Penuela wrote: External Email - Use Caution Hello team! We are trying to load

Re: [Freesurfer] Fwd: vertex MNI305

I think the coordinate circled in the picture is the exact coordinate of the vertex, also in surface ras. The coordinate under "SurfaceRAS" is the coordinate of the current cursor location in surface ras. The slight difference is because the cursor is not exactly on the vertex, but close

Re: [Freesurfer] Surfaces misaligned "Did not find any volume info. Warning: MatrixInverse failed".

Hi Sofia, Would it be possible to send us the volume and one of the surface files you loaded? Best, Ruopeng On 07/24/2018 12:08 PM, Sofia Rodriguez Penuela wrote: External Email - Use Caution Dear Freesurfer team, After loading a volume in Freeview, we try to load surfaces, but

Re: [Freesurfer] fthresh function in tksurfer

> Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > skype: srishti.goel12 > > &

Re: [Freesurfer] Custom color map in Freeview

ur help! Regards Ben On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang mailto:rpw...@nmr.mgh.harvard.edu>> wrote: It looks like a customized look up table will work for your case. You can simply select "Lookup table" as the colormap and load your own lookup table. T

Re: [Freesurfer] changing label outlines in tksurfer

Hi Martin, There is no option to change the thickness of the label outlines right now. I’ll explore the possibilities to add an option for that. Best, Ruopeng > On Jul 9, 2018, at 7:21 AM, Loeffler, Martin > wrote: > >External Email - Use Caution > > Dear Bruce, > >

Re: [Freesurfer] fthresh function in tksurfer

anks, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > skype: sris

Re: [Freesurfer] Freeview not showing images

ddress above, delete this email from your computer, and destroy any copies in any form immediately. *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Ruopeng Wang *Sent:* Friday, June 29, 2018 8:39 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Freeview not showing

Re: [Freesurfer] Freeview not showing images

This looks like a display artifact. Are you running freeview via some kind of X Terminal Emulator on Windows? What if you load a volume? Ruopeng > On Jun 28, 2018, at 7:33 PM, Mark Wagshul > wrote: > > Hi. > > I’m a newbie to Freeview, hoping that this is a simple problem. When I open >

Re: [Freesurfer] questions about freeview quit unexpectly

Would it be possible for you send us the volume file that caused the crash? Best, Ruopeng On 06/26/2018 01:30 PM, 姜时泽 wrote: External Email - Use Caution Hi Rob Many thanks for your feedback. There is no notification pop up. The GUI of freeview just quit. I am not sure what was

Re: [Freesurfer] fthresh function in tksurfer

> Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > skype: srishti.goel12 >

Re: [Freesurfer] brainmask volume disappearing in certain planes in freeview

Hi Rachel, This appears to be some kind of openGL rendering artifact that we are not able to reproduce nor find a definitive solution, unfortunately. It happened to some of us over the years but very very rarely and we were never able to replicate it. It may be a hardware/system glitch. Would

Re: [Freesurfer] fthresh function in tksurfer

Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> skype: srishti.goel12 On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang mailto:rpw...@nmr.mgh.harvard.edu>> wro

Re: [Freesurfer] Freeview surface annotation outline line thickness

Hi Kayle, There is no such option. I'll put it on my list for future improvement. Best, Ruopeng On 05/04/2018 01:09 PM, Kayle Sawyer wrote: The freeview flag "annot_outline=1" is great for viewing results for significant clusters from mri_glmfit-sim. Is there a way to make the outlines

Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

BTW, that only applies to the dev version. Ruopeng > On Apr 13, 2018, at 5:18 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > > Or simply uncheck every item in the look up table except the one you want to > show. > >> On Apr 13, 2018, at

Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

Or simply uncheck every item in the look up table except the one you want to show. > On Apr 13, 2018, at 5:15 PM, Bruce Fischl wrote: > > you can use mri_extract_label on the aseg.mgz to pull out just the label > you want, then load it and the MRI into freeview (if

Re: [Freesurfer] Custom color map in Freeview

It looks like a customized look up table will work for your case. You can simply select "Lookup table" as the colormap and load your own lookup table. To create your own look up table, you can refer to the content of FreeSurferColorLUT.txt file in your freesurfer installation directory.

Re: [Freesurfer] [Freesurfer/Freeview cutting]

Hi, There is no surface cutting function in freeview. But I’m going to add it. Will let you know when I have it ready for testing. Best, Ruopeng > On Mar 7, 2018, at 11:16 PM, Dave Yas wrote: > > Hello, > > Can we cut the surface (for flatting later) in freeview? if

Re: [Freesurfer] Fwd: Freeview update on Mac

Hi Sarah, Drawing an ROI on a surface is a little bit complicated. You will need to have a surface and volume loaded first. Then you create or load a ROI as a volume ROI. On the control panel, there should be a "Map to surface" option, you can map the ROI to the loaded surface. Then you

Re: [Freesurfer] viewing the flatten sheet

Have you tried loading it in freeview? You can load it like this: freeview -f lh.white:patch=lh.flaten.patch.3d Ruopeng On 01/08/2018 10:14 AM, N Saf wrote: Dear experts, I cut the inflated surface in tksurfer and obtain the flatten sheet by mris_flatten but I can not load the

Re: [Freesurfer] Freeview

Can you try creating a symbolic link to libpng16.so.16 in the same location and call it libpng12.so.0? Ruopeng > On Jan 6, 2018, at 5:01 AM, Samir Rekic wrote: > > Hi Ruopeng, > I have the libpng16.so.16 installed on my system > And tried to install the

Re: [Freesurfer] Freeview

Hi Rekic, Do you know what version of libpng installed on your system? Ruopeng > On Jan 5, 2018, at 6:04 AM, Samir Rekic wrote: > > Dear FreeSurfer Team, > I just wanted to ask you a quick question about installing Freeview on a > Ubuntu 17.04, 32-Bit Computer. I

Re: [Freesurfer] Reset view command in freeview

Hi Anna, -viewport option is only to set your main view. So in your case, you should always use '3d'. There is no direct command-line option to set 3D view to a specific orientation. But it can be achieved with -cam option. You can run freeview -h and take a look at the description on how to

Re: [Freesurfer] Freeview problem: ROIs showing in wrong slice when loaded with certain volumes

Hi Sara, Would it be possible to send me the files and the freeview command you ran? Best, Ruopeng > On Dec 6, 2017, at 6:16 PM, Sims, Sara A wrote: > > Hello, > I am having an issues with freeview ROIs. When I use the command line to load > the orig and the ROIs by

Re: [Freesurfer] Freeview display issue in Ubuntu 14/16 VM

Have you installed the latest graphics driver for the virtual machine? Is there any 3D/OpenGL settings you can play with for the virtual machine? Best, Ruopeng On 11/14/2017 11:44 AM, Nicholas Blauch wrote: Hi Freesurfer folks, I’ve recently started using an Ubuntu virtual machine on PC

Re: [Freesurfer] Freeview Crashes!!

What version of freesurfer did you run? It looks like the issue is related to incompatible/missing libraries. Ruopeng > On Nov 10, 2017, at 7:18 AM, vin rasa wrote: > > Dear FS Experts, > > While using updated Freeview in ubuntu 16.04, I reproducibly get two > following

Re: [Freesurfer] Build Freeview on macOS

I believe this has not changed. Best, Ruopeng > On Sep 28, 2017, at 4:14 AM, Aziz Nanthaamornphong > wrote: > > Hi Freesurfer experts, > > Based on this link > https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page >

Re: [Freesurfer] Strange looking dtifit_FA.nii.gz in FreeView

*From:* freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> *Sent:* Tuesday, September 19, 2017 5:39:22 PM *To:* freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] Freeview Strange Behavior

Hi Angel, It appears you're running freeview from FS v5.3, which is over 4 years old. Anyway you can try v6.0 or the latest dev build? Best, Rubin On 09/20/2017 10:19 AM, Torrado Carvajal, Angel wrote: Good morning, We have been experiencing a weird behavior in Freeview when loading non

Re: [Freesurfer] Strange looking dtifit_FA.nii.gz in FreeView

Hi Linnea, I don't see any issue in the screenshots you sent. I couldn't find freeview_T207_dtifit_FA.nii.gz.png in the attachment, either. Also your second screenshot is comparing FA image with a b0 image, which will look somewhat inversed. Best, Ruopeng On 09/19/2017 09:17 AM, Linnea

Re: [Freesurfer] Freeview in FreeSurfer 6.0

I think this may have been fixed in the dev build. Would it possible for you to try the dev build? You can download it here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev > On Aug 21, 2017, at 1:34 AM, Wu Jianxiao (Jadecci)

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

Sure. Please make sure you have as much as spare disk space as you can. > On Aug 10, 2017, at 4:12 PM, Z Hessam <z.hes...@gmail.com> wrote: > > it seems that I should run it again > thank you for your helps > best regards > > On Thu, Aug 10, 2017 at

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

_fh23" command to *.mgz, and then i use the "recon-all -s -all " > command in linux terminal. > > On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote: > How did you put the data o

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

How did you put the data on your drive? > On Aug 10, 2017, at 9:25 AM, Z Hessam <z.hes...@gmail.com> wrote: > > I didn't copy the file, and drive has 3.7GB free space > > On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu > <mailto:rpw.

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

rfer/freesurfer/subjects/bert/mri/T1.mgz > > > On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote: > Hmm, if you run: > > ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz

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