Re: [Freesurfer] freeview command for displaying selected labels

[Ruopeng Wang]

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 labels from the aseg.mgz file using 
> the freeview command line (with FreeSurfer V. 7.1).
> I know that it is possible to manually turn individual labels on and off in 
> the 2D slice view, but I haven’t found a command to do so.
> Is there a way or workaround?
>  
> Thanks,
> René
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Re: [Freesurfer] freeview is RAM greedy in version 7.1.0

[Ruopeng Wang]

Hi Antonin,

I’ve fixed the bug. You can download the latest freeview build here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview 
<https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview>

Best,
Ruopeng

> On May 23, 2020, at 2:08 AM, Antonín Škoch  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi,
> 
> I am testing version
> 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> against version
> freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
> My system is:
> Debian GNU/Linux 8.9 (jessie)
> 
> I tried to merge labels corresponding the same network into one, i.e. I have 
> now only 11 labels, comprising almost all cortical surface. This seems to 
> spare a bit RAM, but still it required approx. 38 GB RAM to load all labels.
> 
> Antonin
> 
> 
> Od: fsbuild  
> 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 14:49, Ruopeng Wang  wrote:
>> 
>> Hi Antonin,
>> 
>> Thanks for the report. We’ll look into this.
>> 
>> Best,
>> Ruopeng
>> 
>>> On May 22, 2020, at 2:42 PM, Antonín Škoch >> <mailto:a...@ikem.cz>> wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> 
>>> Dear experts,
>>> 
>>> I want to use freeview for viewing Gordon surface labels on inflated 
>>> surface with custom coloring. I am using commandline like
>>> 
>>> freeview -viewport 3d -f 
>>> $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0etc
>>>  (the commandline contains 161 labels)
>>> 
>>> I observe that freeview in version 7.1.0 consumes much more RAM than in 
>>> version 6.0, using identical command line. 
>>> The difference is enormous: While in version 6.0 freeview consumes 1.5 GB 
>>> RAM to successfully display all labels, freeview in version 7.1.0 consumes 
>>> all memory available on the server (32 GB RAM) while only about 30 labels 
>>> are actually loaded (then server start to swap and I am forced to kill 
>>> freeview process).
>>> 
>>> Are you aware of such behaviour?
>>> 
>>> Regards,
>>> 
>>> Antonin Skoch
>>> 
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>> 
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> 
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Re: [Freesurfer] freeview is RAM greedy in version 7.1.0

[Ruopeng Wang]

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 coloring. I am using commandline like
> 
> freeview -viewport 3d -f 
> $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0etc
>  (the commandline contains 161 labels)
> 
> I observe that freeview in version 7.1.0 consumes much more RAM than in 
> version 6.0, using identical command line. 
> The difference is enormous: While in version 6.0 freeview consumes 1.5 GB RAM 
> to successfully display all labels, freeview in version 7.1.0 consumes all 
> memory available on the server (32 GB RAM) while only about 30 labels are 
> actually loaded (then server start to swap and I am forced to kill freeview 
> process).
> 
> Are you aware of such behaviour?
> 
> Regards,
> 
> Antonin Skoch
> 
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Re: [Freesurfer] [External] Re: Freesurfer display resolution very low compared to other viewers

[Ruopeng Wang]

Hi Brian,

I honestly can’t tell the difference, even when the high dpi rendering is 
turned on. The volume is low res to begin with. There is a smooth display check 
box you can try in freeview. It will remove the pixelation of the rendering. 

Best
Ruopeng

> On Apr 14, 2020, at 4:28 PM, Renner, Brian  wrote:
> 
> External Email - Use Caution
> Hi Rupoeng!
> 
> Attached is a direct flair opening in same without flags, freeview (L) 
> fsleyes (R), set with 0-168 min-max for each window (fig 1). I did notice a 
> tick box in fsleyes was set to "render in high DPI" was checked (fig 2), so I 
> unchecked it for fig 1. 
> 
> 
> fig 1
> 
> 
> fig 2.
> 
> Perhaps that is the culprit; is there a similar render mode for freeview or 
> is that the driver not optimized as Andrew previously wrote?
> 
> Much 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 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 > <mailto:brian.ren...@cshs.org>> wrote:
>> 
>> External Email - Use Caution
>> Hey Andrew;
>> 
>> Thanks for the response! To answer your questions, yes, We’re all 
>> respectively on Macbook Pro retina displays. I hadn't compared the 
>> visualization on a Windows machine, though I ostensibly could in the near 
>> future. I have loaded up single vs. multiple volumes and noticed what you 
>> say; would it be best to load the hypothetical highest resolution scan 
>> first? ie. freeview -v highest.nii lower.nii. lowest.nii. --trilinear?
>> 
>> An example picture of this is shown below, with a standard 1mm^3 t2 flair 
>> loaded in freeview with a higher resolution t2* as the first loaded scan, 
>> ie. on the left freeview -v t2*file flair --trilinear vs. fsleyes t2*file 
>> flair on the right:
>> 
>> 
>> Fig 1. This is the flair file compared side by side (fv --trilinear vs. 
>> fsleyes, respectively).
>> 
>> 
>> Fig 2. This is the t2*file (0.65mm voxel width), which has both noticeable 
>> quality drop and a different baseline intensity threshold at baseline 
>> between freeview and fsleyes. 
>> 
>> 
>> Fig 3. This is the flair --trilinear vs. flair (noflags) vs. fsleyes flair, 
>> respectively.
>> 
>>  Let me know what you think, and again thank you for the response!
>> 
>> BR
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Hoopes, Andrew 
>> mailto:ahoo...@mgh.harvard.edu>>
>> Sent: Tuesday, April 14, 2020 9:25:08 AM
>> To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: [External] Re: [Freesurfer] Freesurfer display resolution very low 
>> compared to other viewers
>>  
>> Hi Brian,
>>  
>> A couple questions - are you visualizing on a mac retina screen? If so, 
>> there will be a slight decrease from the standard resolution because the 
>> underlying rendering library that we use unfortunately does not support 
>> retina capabilities at this time. Also, are you loading single or multiple 
>> volumes? Freeview uses the first volume loaded as the base image geometry, 
>> and all the following volumes are resampled (if necessary) into this base 
>> geometry using nearest neighbor interpolation. So if you’re working with 
>> different-resolution images, it might help to enable linear interpolation as 
>> the default resampling method by using the `--trilinear` freeview flag. If 
>> that’s not the case, it’d be helpful to see a couple screenshots of the 
>> issue.
>>  
>> Hope that helps,
>> Andrew
>>  
>> From: > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Renner, 
>> Brian" mailto:brian.ren...@cshs.org>>
>> Reply-To: FS Help > <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Date: Monday, April 13, 2020 at 8:54 PM
>> To: FS Help > <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: [Freesurfer] Freesurfer display r

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

[Ruopeng Wang]

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:
> 
> External Email - Use Caution
> Hey Andrew;
> 
> Thanks for the response! To answer your questions, yes, We’re all 
> respectively on Macbook Pro retina displays. I hadn't compared the 
> visualization on a Windows machine, though I ostensibly could in the near 
> future. I have loaded up single vs. multiple volumes and noticed what you 
> say; would it be best to load the hypothetical highest resolution scan first? 
> ie. freeview -v highest.nii lower.nii. lowest.nii. --trilinear?
> 
> An example picture of this is shown below, with a standard 1mm^3 t2 flair 
> loaded in freeview with a higher resolution t2* as the first loaded scan, ie. 
> on the left freeview -v t2*file flair --trilinear vs. fsleyes t2*file flair 
> on the right:
> 
> 
> Fig 1. This is the flair file compared side by side (fv --trilinear vs. 
> fsleyes, respectively).
> 
> 
> Fig 2. This is the t2*file (0.65mm voxel width), which has both noticeable 
> quality drop and a different baseline intensity threshold at baseline between 
> freeview and fsleyes. 
> 
> 
> Fig 3. This is the flair --trilinear vs. flair (noflags) vs. fsleyes flair, 
> respectively.
> 
>  Let me know what you think, and again thank you for the response!
> 
> BR
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > on behalf of Hoopes, Andrew 
> mailto:ahoo...@mgh.harvard.edu>>
> Sent: Tuesday, April 14, 2020 9:25:08 AM
> To: Freesurfer support list  >
> Subject: [External] Re: [Freesurfer] Freesurfer display resolution very low 
> compared to other viewers
>  
> Hi Brian,
>  
> A couple questions - are you visualizing on a mac retina screen? If so, there 
> will be a slight decrease from the standard resolution because the underlying 
> rendering library that we use unfortunately does not support retina 
> capabilities at this time. Also, are you loading single or multiple volumes? 
> Freeview uses the first volume loaded as the base image geometry, and all the 
> following volumes are resampled (if necessary) into this base geometry using 
> nearest neighbor interpolation. So if you’re working with 
> different-resolution images, it might help to enable linear interpolation as 
> the default resampling method by using the `--trilinear` freeview flag. If 
> that’s not the case, it’d be helpful to see a couple screenshots of the issue.
>  
> Hope that helps,
> Andrew
>  
> From:  > on behalf of "Renner, Brian" 
> mailto:brian.ren...@cshs.org>>
> Reply-To: FS Help  >
> Date: Monday, April 13, 2020 at 8:54 PM
> To: FS Help  >
> Subject: [Freesurfer] Freesurfer display resolution very low compared to 
> other viewers
>  
> External Email - Use Caution
> Hello all! 
>  
> Inaugural message to the list; I will attempt to be brief with the project 
> description.
>  
> The setup is consistent between both versions 6.0.0 and 7.0.0-beta, run on a 
> high performance cluster, accessed through macOS terminal + Xquartz, most 
> recent versions all.
>  
> As it stands, our group is attempting to do subfield analysis of hippocampal 
> analysis and lesion measurement in MS subjects. We have noticed that there is 
> a major discrepancy of resolutions between files, which has irked some of our 
> physicians undertaking the lesion measurement. We need to resolve the lesions 
> down to 3mm and have noticed the quality between freeview and fsleyes of the 
> same nifti files will yield much lower display resolution. This is true for 
> most scans, though it has been compared using 1mm T2 FLAIR sequences as well 
> as T2* sequences with 0.65mm voxel space. I have been attempting to find a 
> workaround as the current solution for the physicians is to look at the files 
> in fsleyes and then measure them with the ruler tool in freeview. I can send 
> supporting pictures as necessary. 
>  
> Thank you in advance for any thoughts you may have!
>  
> BR
>  
> --
> Brian Renner, MD
> Research Associate, Neurology 
> brian.ren...@cshs.org 
> 
> Cedars-Sinai
> 127 S. San Vicente Blvd, Suite A6600  :  Los Angeles CA 90048
> office 310-423-1589  :  mobile 310-658-3492  :  cedars-sinai.org 
>  
>  
> 
> 
> IMPORTANT WARNING: This message is intended for the use of the person or 
> entity to which it is addressed and may contain information that is 
> privileged and confidential, the disclosure of which is governed by 
> applicable law. If the reader of this me

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

[Ruopeng Wang]

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:
freeview -f lh.inflated:patch=patch_file

Best,
Ruopeng


> On Apr 7, 2020, at 9:24 PM, Devavrat Vartak PhD  wrote:
> 
> External Email - Use Caution
> 
> 
> Hello Freesurfer developers,
> 
> Thank you for developing Freesurfer!   
> 
> I am postdoc at UC Berkeley and I am using Freesurfer 6.0 to create flat maps 
> on which I draw my ROI's. The flat maps/patches are created in TKSURFER. 
> However, I typically use Freeview to visualise my volumes and inflated 
> surfaces, overlay data etc. 
> I am trying to open flatmap maps in freeview but I am not able to. I was 
> wondering if it was possible to load flatmaps in freeview and draw ROI's on 
> them and overlay my data?
> 
> OS: MacBook OS
> 
> Thank you.
> 
> Best,
> Devavrat
> 
> -- 
> Devavrat Vartak, PhD
> Postdoctoral Researcher
> 
> Helen Wills Neuroscience Institute and School of Optometry
> 
> Mailing address:
> 360 Minor Hall #2020
> University of California, Berkeley
> Berkeley, CA, 94720-2020
> USA
> 
> Website: www.dvartak.com 
> 
> Email: 
> dvar...@berkeley.edu 
> devavratvar...@gmail.com 
> 
> 
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Re: [Freesurfer] (no subject)

[Ruopeng Wang]

I don’t think look up table works with negative indices. It was mainly designed 
for label volumes. 

Ruopeng

> On Apr 6, 2020, at 10:35 AM, Peng Liu  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Ruopeng,
> 
> Thank you for your reply.
> 
> I have also tried NIH and JET, but with negative scale, the entire image will 
> turn into one same color as if there is some error.
> 
> Meanwhile the reason of me trying to create .lut map is because I want five 
> colours and five colours only...
> 
> Is there any specific reason 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 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 > <mailto:claudialiu1...@gmail.com>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Dear Freesurfer experts,
>> 
>> I am trying to customize a colour map of my own, with five colours and scale 
>> from -12.5 to 12.5, since when using Heat (with default options), the scale 
>> is correct but it is shown in only four colours.
>> 
>> However after I created the .lut file (attached below), when loading it into 
>> freeview, the colour scale is from 0 to 6.
>> 
>> 
>> 
>> Does this mean I should also include scale information in the .lut file?
>> 
>> Any help would be much appreciated.
>> 
>> Peng Liu
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Re: [Freesurfer] (no subject)

[Ruopeng Wang]

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 Email - Use Caution
> 
> 
> Dear Freesurfer experts,
> 
> I am trying to customize a colour map of my own, with five colours and scale 
> from -12.5 to 12.5, since when using Heat (with default options), the scale 
> is correct but it is shown in only four colours.
> 
> However after I created the .lut file (attached below), when loading it into 
> freeview, the colour scale is from 0 to 6.
> 
> 
> 
> Does this mean I should also include scale information in the .lut file?
> 
> Any help would be much appreciated.
> 
> Peng Liu
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Re: [Freesurfer] Tkmedit gui download

[Ruopeng Wang]

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 freeview which can do what tkmedit 
did and more. 

Best,
Ruopeng

> On Apr 1, 2020, at 6:39 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
>  wrote:
> 
> Hi all,
> 
> I am still trying to adapt to working from home, and I am forced to work with 
> incredibly slow download speeds. I am trying to download FS6.0 for mac for 
> the sole purpose of using tkmedit, rather than the entire toolbox, just so I 
> can edit brains (I anticipate downloading FS6.0 for mac in my house would 
> take like 36 hours). Can someone provide me a link to download just the 
> necessary codes for tkmedit in macs? I would greatly appreciate this. 
> Thanks,
> 
> Victor Zeng
> Beth Israel Deaconess Medical Center
> Keshavan Lab
> --
> 
> 
> This message is intended for the use of the person(s) to whom it may be 
> addressed. It may contain information that is privileged, confidential, or 
> otherwise protected from disclosure under applicable law. If you are not the 
> intended recipient, any dissemination, distribution, copying, or use of this 
> information is prohibited. If you have received this message in error, please 
> permanently delete it and immediately notify the sender. Thank you.
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Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations

[Ruopeng Wang]

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:
> 
> External Email - Use Caution
> 
> 
> Hi Ruopeng,
> 
> I entered the full path for the transformation file, and this is what I’m 
> seeing in freeview (screenshot attached). Is it possible to edit the 
> talairach registrations in freeview similar to how they could be edited in 
> tkmedit, or can freeview only be used for looking at talairach registrations?
> 
> Thanks again,
> Rachel
> 
> 
> 
> 
> 

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

[Ruopeng Wang]

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 and I'm trying to use freeview to 
> check talairach registrations - I've always used tkmedit, so I am running 
> into some issues with the command line for viewing the transform.
> 
> When I run the following command: 
>   freeview -v /mri/T1.mgz \
> /mri/brainmask.mgz:reg=/mri/transforms/talairach.xfm
>  I get the following errors:
> 
> regio_read_mincxfm: No such file or directory
> ERROR: could not read /mri/transforms/talairach.xfm
> ERROR: could not read /mri/transforms/talairach.xfm
> 
> Thanks in advance!
> 
> Rachel
> 
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Re: [Freesurfer] Freeview CLI feature request

[Ruopeng Wang]

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 following features as command line flags to 
> FreeView?
>  
> 1) Set opacity for a surface
> It is currently only possible via CLI to set opacity for volumes, surface 
> overlays, and labels, but not for the surface itself.
>  
> 2) Set smoothing iterations for isosurfaces
> This can only be done in the GUI, not yet via the CLI.
>  
> Thank you for your consideration.
>  
> - Vincent
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Re: [Freesurfer] overlay threshold in freeview

[Ruopeng Wang]

Hi Rachele,

The automatic threshold setting of overlay in freeview was meant to just 
quickly set an initial value for user to see. As I check the code, the high 
threshold is set as the maximum value, the low is set simply as the mid point 
between min and max values. It wasn’t meant to be optimal but I think it can 
definitely be improved. I will update it to 50th percentile in the development 
version.

Best,
Ruopeng

> On Mar 17, 2020, at 4:27 AM, Rachele Sanfelici  wrote:
> 
> External Email - Use Caution
> 
> 
> Dear Freesurfer experts,
> 
> Sorry for catching up so late, you can imagine the situation here in Europe..
> 
> Thank you Ruopeng for your answer! What I’m trying to figure out, though, is 
> how Freeview automatically sets the threshold for overlays, not how to set it 
> myself.
> I tried several combinations with my data (median, mean, 50th percentile), 
> but none gives me the same result as the freeview automatic threshold. Could 
> you please give me more information or a reference? Are you e.g. excluding 
> the highest values (to avoid outliers) or truncating the values after e.g. 8 
> numbers 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:
>> 
>> 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:
>>> External Email - Use Caution
>>> 
>>> Dear Freesurfer experts,
>>> 
>>> I created .mgh files from a dimensionality reduction analyses (similar to 
>>> parcels from a known parcellation). These matrices have low values near to 
>>> 0. When I overlay each of the .mgh file in freeview, it gets automatically 
>>> thresholded with what seemed to me the median or mean of all the vertices' 
>>> values (i.e., when looking at the "configure overlay" option)--however, 
>>> this is not the case. 
>>> Thus, I wanted to ask how the threshold is precisely set, so that I can 
>>> automate and incorporate it in other scripts for binarizing my matrices.
>>> 
>>> Thanks a lot in advance for your help,
>>> Rachele
>>> 
>>> 
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> 
> Rachele Sanfelici, Psychologin 
> PRONIA Früherkennungsambulanz („Personalized
> Prognostic Tools for Early Psychosis Management“)
>  
> Klinik und Poliklinik für Psychiatrie und Psychotherapie
> Ludwig-Maximilians-Universität München
> Nußbaumstr. 7, 80336 München
> Tel.: +49 (0)89/4400- 52731
> Homepage:http://pronia.eu <http://pronia.eu/>​​
> 
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Re: [Freesurfer] overlay threshold in freeview

[Ruopeng Wang]

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:


External Email - Use Caution

Dear Freesurfer experts,

I created .mgh files from a dimensionality reduction analyses (similar 
to parcels from a known parcellation). These matrices have low values 
near to 0. When I overlay each of the .mgh file in freeview, it gets 
automatically thresholded with what seemed to me the median or mean of 
all the vertices' values (i.e., when looking at the "configure 
overlay" option)--however, this is not the case.
Thus, I wanted to ask how the threshold is precisely set, so that I 
can automate and incorporate it in other scripts for binarizing my 
matrices.


Thanks a lot in advance for your help,
Rachele

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Re: [Freesurfer] freeview failed to load Surface overlay

[Ruopeng Wang]

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 interested in), age and genetic scores (the 
latter of which I am interested in) included in the glm. Atm I am 
using a DODS model (0 0 0 0 0.5 0.5), however, as I am actually not at 
all interested in gender differences...would it be smarter to use a 
DOSS model? (0 0 1 ?).


And a question regarding freeview: I always get "failed to load 
Surface overlay"/"could not open file" errors when trying to overlay 
calculated sig.mgh (or beta.mgh or pretty much anything) on the 
fsaverage.inflated surface. From these  error messages I cannot really 
spot the issue- I guess it might be some kind of matrix dimension 
mismatch? Which confuses me, as I resampled the data to the fsaverage 
brain...?


I ran:

1. mris_preproc --fsgd 1234.fsgd --cache-in thickness.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.1234.10.mgh


2. mri_glmfit --y lh.1234.thickness.10.mgh --fsgd 1234.fsgd --C 
1234.mtx --surf fsaverage lh --cortex --glmdir lh.1234.glmdir


--> freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh

When I launch freeview and try to overlay sig.mgh manually, I get 
"Correlation data does not match with surface". Does this have 
something to do with the "apply registration option" and if so, what 
would I have to select here? (since the data should already be 
registered to fsaverage...?).


Thanks a lot,

Meike




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Re: [Freesurfer] Cannot load overlay through GUI

[Ruopeng Wang]

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 FreeSurfer experts:
>
> I encountered a weird problem when trying to load overlay through the 
> Freeview GUI. I opened a surface file through terminal command “freeview -f 
> lh.pial”, and then in the GUI I clicked Overlay -> load generic -> Select 
> overlay file. After I selected the overlay file Freeview stopped responding. 
> The following messages showed up in terminal:
>
> 2020-01-29 16:13:31.469 Freeview[1067:24667] warning:  0x7fee5240bf70 com.apple.appkit.xpc.openAndSavePanelService ((null)) 
> NSServiceViewControllerForTouchBarItem> determined it was necessary to 
> configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view 
> vibrancy
> 2020-01-29 16:13:31.491 Freeview[1067:24667] warning:  0x7fee5240ddd0 com.apple.appkit.xpc.openAndSavePanelService ((null)) 
> NSServiceViewControllerForTouchBarItem> determined it was necessary to 
> configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view 
> vibrancy
>
> The first message showed up when I clicked on the folder icon to select 
> overlay file, and the second message showed up when I clicked “Open” after I 
> selected overlay file.
>
> However, if I just ran “freeview -f rh.pial:overlay=”, the 
> viewer could open the overlay file without problem.
>
> Is there any fix for this GUI problem? I am on macOS Catalina Version 10.15.2.
>
> Thank you,
> Fengdan
>
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Re: [Freesurfer] Freeview froze when trying to open volume file

[Ruopeng Wang]

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 freeview froze when I tried 
to select and open a new volume file.
This started after I upgraded mac OS X to Catalina. Until that I have 
been using freeview fine for five years.


Error message said

Last login: Thu Jan 23 13:43:03 on ttys000
[tup09900bj11:~] tomotarui% setenv FREESURFER_HOME 
/Applications/freesurfer

[tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR           /usr/local/fsl
[tup09900bj11:~] tomotarui% freeview
2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been 
exited prematurely - check for a reentrant call to endModalSession:


I do have read permissions for those volume files when I checked with 
ls -l and mri_info.
I have tried cleaned up and reinstall freesurfer, which did not solve 
the problem.
It may be unique to my computer, but I would appreciate very much for 
any recommendation.

Tomo


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Re: [Freesurfer] Freeview Surface Loading View Center

[Ruopeng Wang]

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 7:22 PM, Mingjian He  wrote:
> 
> Hi,
> 
>   When using Freeview to load a surface file without volume, how does 
> Freeview set the initial view center and cursor position? I’ve checked mid 
> point of xyz ranges, centroid of vertices, and median. None of these gives me 
> the initial SurfaceRAS values when opening the surface with Freeview. 
> 
>   Thank you! 
> 
> Best,
> Alex
> External Email - Use Caution
> 
> 
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Re: [Freesurfer] Freeview - command-line label sub-option "opacity" does not work

[Ruopeng Wang]

I’ll add the option for surface labels.

> On Dec 30, 2019, at 2:02 PM, Antonin Skoch  wrote:
> 
> 
> External Email - Use Caution
> 
> Hi Ruopeng,
> 
> the command is something like:
> 
> freeview  -f rh.inflated:label=my.label:opacity=0.5
> 
> 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?
> 
> Antonin
> 
> 
> Od: Ruopeng Wang  
> Komu: Antonin Skoch , Freesurfer support list 
>  
> Odesláno: 30.12.2019 19:50 
> Předmět: 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 sub-option flag 'opacity'.
>> 
>> I am using most recent dev version (30 dec 2019).
>> 
>> Could you please check that?
>> 
>> Regards,
>> 
>> Antonin Skoch
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Re: [Freesurfer] Freeview - command-line label sub-option "opacity" does not work

[Ruopeng Wang]

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 sub-option flag 'opacity'.
> 
> I am using most recent dev version (30 dec 2019).
> 
> Could you please check that?
> 
> Regards,
> 
> Antonin Skoch
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Re: [Freesurfer] Save output as attach file

[Ruopeng Wang]

You can go ahead and try it.

Ruopeng

> On Dec 24, 2019, at 12:09 PM, Nader Razmara  wrote:
> 
> External Email - Use Caution
> 
> 
> Dear Ruopeng
> Thanks a lot for what you did.
> But I have installed and work with freesurfer Disk image 5.3 not freesurfer 
> 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 called “Boundary” in menu Tools -> Volume 
> Filters. You can apply it to your volume and then save volume as. Here is an 
> instruction on how to update to the latest freeview:
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview 
> <https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview>
> 
> Best,
> Ruopeng
> 
> 
>> On Dec 23, 2019, at 10:59 AM, Nader Razmara > <mailto:naderi...@gmail.com>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Hi Roupeng
>> Can i hope you do it soon.
>> It is an important part of my phd thesis.
>> Best regards 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 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?
>> >
>> > cheers
>> > Bruce
>> >
>> >
>> > On Sat, 21 Dec 2019, Nader Razmara wrote:
>> >
>> >>
>> >> External Email - Use Caution
>> >>
>> >> Thanks a lot.As yuo see in attach i have opened an aseg.mgz which i have
>> >> made with recon-all. In freeview i thicked lookup table and outline. 
>> >> As you
>> >> see this is appearance of what i did. Now i want to save this as a 
>> >> new mgz
>> >> file which when i opened it with other image softwares i have this
>> >> apearanse.
>> >> Is it possibe?
>> >> Best regards
>> >> Nader
>> >> Neuroimaging phd student
>> >>
>> >> On 21 Dec 2019 18:36, "Bruce Fischl" > >> <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>> >>   sorry, can you clarify what you mean? Isn't the attachment
>> >>   already a
>> >>   saved output of freeview? I don't understand what you are trying
>> >>   to do
>> >>
>> >>   cheers
>> >>   Bruce
>> >>   On
>> >>   Sat, 21 Dec 2019, Nader Razmara wrote:
>> >>
>> >>   >
>> >>   > External Email - Use Caution
>> >>   >
>> >>   > Dear I want to save output of freeview as attach file. Which
>> >>   is a
>> >>   > segmentation after thick colourmap ad lookptable and thick
>> >>   outline.
>> >>   > Best regards
>> >>   >
>> >>   >
>> >> >___
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>> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >>
>> >>
>> >>
>> >>
>> ___
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Re: [Freesurfer] Save output as attach file

[Ruopeng Wang]

Hi Nadar,

I’ve added a new volume filter called “Boundary” in menu Tools -> Volume 
Filters. You can apply it to your volume and then save volume as. Here is an 
instruction on how to update to the latest freeview:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview 
<https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview>

Best,
Ruopeng


> On Dec 23, 2019, at 10:59 AM, Nader Razmara  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Roupeng
> Can i hope you do it soon.
> It is an important part of my phd thesis.
> Best regards 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 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?
> >
> > cheers
> > Bruce
> >
> >
> > On Sat, 21 Dec 2019, Nader Razmara wrote:
> >
> >>
> >> External Email - Use Caution
> >>
> >> Thanks a lot.As yuo see in attach i have opened an aseg.mgz which i have
> >> made with recon-all. In freeview i thicked lookup table and outline. 
> >> As you
> >> see this is appearance of what i did. Now i want to save this as a 
> >> new mgz
> >> file which when i opened it with other image softwares i have this
> >> apearanse.
> >> Is it possibe?
> >> Best regards
> >> Nader
> >> Neuroimaging phd student
> >>
> >> On 21 Dec 2019 18:36, "Bruce Fischl"  >> <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
> >>   sorry, can you clarify what you mean? Isn't the attachment
> >>   already a
> >>   saved output of freeview? I don't understand what you are trying
> >>   to do
> >>
> >>   cheers
> >>   Bruce
> >>   On
> >>   Sat, 21 Dec 2019, Nader Razmara wrote:
> >>
> >>   >
> >>   > External Email - Use Caution
> >>   >
> >>   > Dear I want to save output of freeview as attach file. Which
> >>   is a
> >>   > segmentation after thick colourmap ad lookptable and thick
> >>   outline.
> >>   > Best regards
> >>   >
> >>   >
> >> >___
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> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >>
> >>
> >>
> >>
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Re: [Freesurfer] Save output as attach file

[Ruopeng Wang]

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?
>
> cheers
> Bruce
>
>
> On Sat, 21 Dec 2019, Nader Razmara wrote:
>
>>
>> External Email - Use Caution
>>
>> Thanks a lot.As yuo see in attach i have opened an aseg.mgz which i have
>> made with recon-all. In freeview i thicked lookup table and outline. 
>> As you
>> see this is appearance of what i did. Now i want to save this as a 
>> new mgz
>> file which when i opened it with other image softwares i have this
>> apearanse.
>> Is it possibe?
>> Best regards
>> Nader
>> Neuroimaging phd student
>>
>> On 21 Dec 2019 18:36, "Bruce Fischl"  wrote:
>>   sorry, can you clarify what you mean? Isn't the attachment
>>   already a
>>   saved output of freeview? I don't understand what you are trying
>>   to do
>>
>>   cheers
>>   Bruce
>>   On
>>   Sat, 21 Dec 2019, Nader Razmara wrote:
>>
>>   >
>>   > External Email - Use Caution
>>   >
>>   > Dear I want to save output of freeview as attach file. Which
>>   is a
>>   > segmentation after thick colourmap ad lookptable and thick
>>   outline.
>>   > Best regards
>>   >
>>   >
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>>
>>
>>
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Re: [Freesurfer] Trouble running Freeview from Mac Terminal

[Ruopeng Wang]

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 been having trouble running freeview from the Mac OS terminal 
via XQuartz on my laptop.  I have seen the problem with both Mac OS 
10.15.1 (Catalina) and the previous version of Mac OS.  I get the 
error copied below.


I am however able to run other GUIs such as fslview.  The problem 
seems to be unique to freeview as best I can tell.


Has anyone else ever experienced this error?

--- Jason

> [deepbrain:~] (nmr-stable60-env) freeview

> X Error: BadValue (integer parameter out of range for operation) 2

> Extension:149 (Uknown extension)

> Minor opcode: 3 (Unknown request)

> Resource id:  0x0

> Abort (core dumped)

> [deepbrain:~] (nmr-stable60-env)

>



Jason Stockmann

Assistant Professor in Radiology

A. A. Martinos Center for Biomedical Imaging

Massachusetts General Hospital

Charlestown, MA 02129

jstockm...@mgh.harvard.edu 

+1 315 450 3309


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Re: [Freesurfer] V1 length

[Ruopeng Wang]

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 shift and move your mouse cursor over on the path, 
you should see the length of the path on the Info panel at the bottom.



Best,

Ruopeng


On 11/25/19 5:36 AM, Melissa Wright wrote:


External Email - Use Caution

Hi everyone,

I'm currently using mris_divide_parcellation to create segmentations 
of V1 by dividing along its long axis. However, I would like to 
extract the length of this long axis (in mm), in order to compare it 
with CMF. Would anyone know how best to go about this?


Sorry if there's an obvious answer! I have tried looking online and at 
the function scripts, but no luck.


Thank you and best wishes,

Melissa E Wright

*Melissa E Wright, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research Imaging Centre (CUBRIC), School of 
Psychology


Cardiff University

Maindy Road

Cardiff   CF24 4HQ

UK

/*Tel*/: +44 (0)29 208 20275

/*Email*/: wrigh...@cardiff.ac.uk 

/*Web*/: Cardiff University webpage 



*Twitter: *@MEW_Neuro



*Melissa E Wright, MSc*

*Myfyrwraig PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd CF24 4HQ

DU

/*Ffôn*/: +44 (0)29 208 20275

/*E-bost*/: wrigh...@caerdydd.ac.uk 


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

[Ruopeng Wang]

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 tying to load multiple volumes in Freeview with a 
single option applied to all the volumes.


For example, I would like to set grayscale window as min=0 and max=100 
for all volumes. Is there a simple command line which does that 
efficiently?


The command line below works if I provide the option for each volume:

freeview -v sitename/mri/subj0401/brainmask.mgz:grayscale=0,100 \
sitename/mri/subj0402/brainmask.mgz:grayscale=0,100\
... \
sitename/mri/subj0425/brainmask.mgz:grayscale=0,100


However, the command line something like this does not:

freeview -v sitename/mri/subj*/brainmask.mgz:grayscale=0,100


Thanks in advance,

Ikbeom

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Re: [Freesurfer] freeview command line options

[Ruopeng Wang]

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 found a bug in freeview:

I'm using the overlay_color option with freeview. Specifically I am 
trying to use both the "truncate" and "inverse" options in a command 
line call to freeview for a pipeline I am building. The documentation 
says that I can apply more than one, delimited by commas  however 
I have found that if I attempt to use both truncate and inverse, it 
seems to be only applying whichever one appears last on the list.


In an interactive instance of freeview, doing everything manually, I 
have no problems. Just seems to be an issue with the command line 
call. Any suggestions on how I might proceed in this case?


-Eli

Houston Methodist. Leading Medicine.

Houston Methodist is ranked by /U.S. News & World Report/ as the No. 
1 hospital in Texas and among the top 20 hospitals nationwide. 
Houston Methodist is the only nationally ranked Honor Roll hospital 
in the state and is designated as a Magnet hospital for excellence in 
nursing.



houstonmethodist.org | 
twitter.com/MethodistHosp  | 
facebook.com/HoustonMethodist 



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Re: [Freesurfer] freeview command line options

[Ruopeng Wang]

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 use both the "truncate" and "inverse" options in a command 
line call to freeview for a pipeline I am building. The documentation 
says that I can apply more than one, delimited by commas  however 
I have found that if I attempt to use both truncate and inverse, it 
seems to be only applying whichever one appears last on the list.


In an interactive instance of freeview, doing everything manually, I 
have no problems. Just seems to be an issue with the command line 
call. Any suggestions on how I might proceed in this case?


-Eli

Houston Methodist. Leading Medicine.

Houston Methodist is ranked by /U.S. News & World Report/ as the No. 1 
hospital in Texas and among the top 20 hospitals nationwide. Houston 
Methodist is the only nationally ranked Honor Roll hospital in the 
state and is designated as a Magnet hospital for excellence in nursing.



houstonmethodist.org | 
twitter.com/MethodistHosp  | 
facebook.com/HoustonMethodist 


***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston 
Methodist and/or its relevant affiliates and may contain restricted 
and privileged material for the sole use of the intended recipient(s). 
Any review, use, distribution or disclosure by others is strictly 
prohibited. If you are not the intended recipient (or authorized to 
receive for the recipient), please contact the sender and delete all 
copies of the message. Thank you.



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Re: [Freesurfer] Freeview error

[Ruopeng Wang]

Is your work disk full?

On 9/17/19 10:22 AM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution


I tried in the command window where I started freeview but nothing 
happened. This is the output


miguel@miguel-VirtualBox:~$ ls 
/usr/local/freesurfer/subjects/4227/mri/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 5:11 PM, Miguel Ángel Rivas Fernández
mailto:miguelrivasf...@gmail.com>> wrote:

External Email - Use Caution


Dear Ruopeng,

I put that command in the 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 lun., 16 sept. 2019 a las 22:58, Ruopeng Wang
(mailto:rpw...@nmr.mgh.harvard.edu>>) escribió:

If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng

On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution

Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I
obtained this error:


mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz,
-1): could not open file
MRIread failed: Unable to read from
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz,
-1): could not open file

Any suggestion about what could be the problem?, maybe the
write permissons of the freesurfer folder?

I am using the
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
version that is installed in a Ubuntu 18.04 virtual machine.
It is very strange because few weeks ago everything it was
working correctly.

Thanks in advance.


Best regards,
-- 
*Miguel Ángel Rivas Fernández*


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*Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Freeview error

[Ruopeng Wang]

Can you run the command in the command window that you start freeview?

Ruopeng

> On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández 
>  wrote:
> 
> External Email - Use Caution
> 
> 
> Dear Ruopeng, 
> 
> I put that command in the 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 lun., 16 sept. 2019 a las 22:58, Ruopeng Wang ( <mailto:rpw...@nmr.mgh.harvard.edu>>) escribió:
> If you run:
> 
> ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
> 
> What does it show? 
> 
> Ruopeng
> 
> On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
>> External Email - Use Caution
>> 
>> Dear Freesurfer devs,
>> 
>> I tried to open the brainmask.mgz file in freeview but I obtained this error:
>> 
>> 
>> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could 
>> not open file
>> MRIread failed: Unable to read from 
>> /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
>> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could 
>> not open file
>> 
>> Any suggestion about what could be the problem?, maybe the write permissons 
>> of the freesurfer folder? 
>> 
>> I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
>> version that is installed in a Ubuntu 18.04 virtual machine. It is very 
>> strange because few weeks ago everything it was working correctly. 
>> 
>> Thanks in advance.
>> 
>> 
>> Best regards,
>> -- 
>> Miguel Ángel Rivas Fernández
>> 
>> 
>> ___
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>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>___
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> 
> -- 
> Miguel Ángel Rivas Fernández
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Re: [Freesurfer] Freeview error

[Ruopeng Wang]

If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng

On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution

Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I obtained this 
error:



mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): 
could not open file
MRIread failed: Unable to read from 
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): 
could not open file


Any suggestion about what could be the problem?, maybe the write 
permissons of the freesurfer folder?


I am using the 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that 
is installed in a Ubuntu 18.04 virtual machine. It is very strange 
because few weeks ago everything it was working correctly.


Thanks in advance.


Best regards,
--
*Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] 001 vs brainmask views in freeview

[Ruopeng Wang]

Yes, these two volume are aligned. But they are sliced differently. When 
you display a single volume alone in freeview, it is by default 
displayed in its native slice orientation.


Ruopeng

On 9/16/19 3:39 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

I’m still a little confused. When I open up the brainmask.mgz in 
freeview I see the following. It is rotated compared to the native 
001.mgz below.


I then open the 001.mgz with freeview in a NEW terminal (seperate 
session),  I get the following.  Should thy not be the same orientation?


*From:*freesurfer-boun...@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 that the pixel data don't get resampled 
(unless you force it with '-r' flag to resample it in standard RAS).


Ruopeng

On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote:

*External Email - Use Caution *

Thanks for info.

If I open only the brainmsk.mgz only from a new terminal it is
rotated and not in its native orientation (which is 001’s
orientation).

Why does it not appear to be in native space in freeview?

Jim

*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*Ruopeng Wang
*Sent:* Monday, September 16, 2019 11:51 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto: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 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 -trilinear

Ruopeng

On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote:

*External Email - Use Caution *

Hi all,

I ran a 2yo subject through FS6.0 using ‘recon-all -i
/firstdicom.dcm -all’ and the output segmentations and
surfaces looks good.

Can someone explain why I see different alignments when I view
the 001.mgz and brainmask.mgz files in freeview, depending on
the order files are opened.

001.mgz AND brainmask.mgz -- 001 opened first in freeview
followed by brainmask.mgz. Alignemnts OK but brainmask looks
grainy.

Brainmask.mgz opened only in a new terminal. Rotated and looks
smoother than brainmask above.



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Re: [Freesurfer] 001 vs brainmask views in freeview

[Ruopeng Wang]

The first volume is always displayed in its original orientation where 
pixel data are stored. So that the pixel data don't get resampled 
(unless you force it with '-r' flag to resample it in standard RAS).


Ruopeng

On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Thanks for info.

If I open only the brainmsk.mgz only from a new terminal it is rotated 
and not in its native orientation (which is 001’s orientation).


Why does it not appear to be in native space in freeview?

Jim

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf 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 
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 -trilinear

Ruopeng

On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote:

*External Email - Use Caution *

Hi all,

I ran a 2yo subject through FS6.0 using ‘recon-all -i
/firstdicom.dcm -all’ and the output segmentations and surfaces
looks good.

Can someone explain why I see different alignments when I view the
001.mgz and brainmask.mgz files in freeview, depending on the
order files are opened.

001.mgz AND brainmask.mgz -- 001 opened first in freeview followed
by brainmask.mgz. Alignemnts OK but brainmask looks grainy.

Brainmask.mgz opened only in a new terminal. Rotated and looks
smoother than brainmask above.



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sensitive nature. If you are not the intended recipient, be
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The materials in this message are private and may contain Protected 
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Re: [Freesurfer] 001 vs brainmask views in freeview

[Ruopeng Wang]

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 -trilinear

Ruopeng

On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Hi all,

I ran a 2yo subject through FS6.0 using ‘recon-all -i /firstdicom.dcm 
-all’ and the output segmentations and surfaces looks good.


Can someone explain why I see different alignments when I view the 
001.mgz and brainmask.mgz files in freeview, depending on the order 
files are opened.


001.mgz AND brainmask.mgz -- 001 opened first in freeview followed by 
brainmask.mgz. Alignemnts OK but brainmask looks grainy.


Brainmask.mgz opened only in a new terminal. Rotated and looks 
smoother than brainmask above.




The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

[Ruopeng Wang]

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 Caution

Hi Doug and Ruopeng,
thanks a lot for your advice!
Is there a way to display a meaningful legend? In tksurfer/rtview, we 
get a linear legend that does not seem to make much sense and in 
freeview we typically do not get anything when we choose color wheel 
and then click on the legend button.

Thanks! Caspar


Am Di., 10. Sept. 2019 um 17:23 Uhr schrieb Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>:


When you run rtview, it will run tksurfer. To get to the color wheel,
open View->Configure->Overlay, then select "Color Wheel" under the
"Color Scale" tab.

On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi Doug and Roupeng,
> did you already have the chance to look into the question how to
> display the color wheel with rtview and/or freeview?
> Thank you! Caspar
>
> Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik
> mailto:cschwie...@mail.rockefeller.edu>
> >>:
>
>     External Email - Use Caution
>
>     Hi Doug and Ruopeng,
>     it would be amazing if you could dig out the information on
how to
>     display the color wheel.
>     Looking forward to what you find!
>     Caspar
>
>
>     Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas
N.,Ph.D.
>     mailto:dgr...@mgh.harvard.edu>
>>:
>
>         Hi Caspar, sorry for the delay. I have not used the
retinotoy
>         stream in a long, long time so I don't know off the top
of my
>         head. I'll have to look into it. tksurfer (from rtview) does
>         have a way to display using the color wheel, but I don't
>         remember how to do it.
>
>         Ruopeng, can freeview display using a color wheel?
>
>         On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>>
>>         External Email - Use Caution
>>
>>         Hi!
>>         I wanted to ask again whether there is a way to display the
>>         color wheel in rtview and/or freeview. We are debugging our
>>         analyses and it would be immensely helpful to have a legend
>>         that specifies the color assignments.
>>         Thank you,
>>         Caspar
>>
>>         On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
>>         mailto:cschwie...@rockefeller.edu>
>>         >> wrote:
>>
>>             Hi!
>>             I am following up on this thread trying to
understand how
>>             to make the color wheel visible in rtview, or, if
>>             necessary, in freeview.
>>             Thank you! Caspar
>>
>>
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Re: [Freesurfer] freeview crash -- petsc error when opening volume

[Ruopeng Wang]

eeview running on Ubuntu 18, and ultimately the same errors 
occur. As well, I replicated this behavior on a separate Ubuntu 18 
machine in the environment, this time using a different lab's 
T1/brainmask/surface files. It would definitely seem like there is 
some sort of hard incompatibility with newer versions of freeview 
and loading surface files on top of volumes in Ubuntu 18.


For what it's worth, it's not evident that any other part of FS has 
an issue; all CLI tools seem to work just fine.


Tristan


*From:*TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
*Sent:*Friday, August 23, 2019 11:38 AM
*To:*Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*Re: [Freesurfer] freeview crash -- petsc error when 
opening volume

Good morning Ruopeng, thank you for your continued assistance!

Unfortunately, I get the same error using the CentOS6 dev version.. 
I tried the CentOS7 dev version, however this led to a series of 
library errors, the majority of which are unsolvable on Ubuntu 18 
without individually compiling each necessary library (sym-linking 
newer libraries does not work).


I wanted to ensure I provide the most details possible, so I also 
installed FS 5.3.0 and tested the files...interestingly, they opened 
just fine, no errors at all.


This leads me to believe there is some strange incompatibility 
between Ubuntu 18 and the 6.x/dev version of FS (at least when it 
comes to surface files), specifically related to PETSC. Is there 
anything 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 Tristan,

Thanks for the files. I have no problem loading them with the latest 
dev build and stable 6.0 build. I do not have an Ubuntu system, though.


If I’m not mistaken you use dev version of freeview binary along 
with stable 6.0 FS binary. Is that correct? Is there any chance you 
can try installing the whole FS dev package?


Ruopeng

On Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH <mailto:tpaut...@wisc.edu>> wrote:


External Email - Use Caution
Ruopeng,

I've uploaded the files to the FTP drop 
(transfer/incoming/freesurfer_data.tar.gz). The command my user is 
running against these files is:


freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow 
lh.pial:edgecolor=magenta rh.white:edgecolor=yellow 
rh.pial:edgecolor=magenta


We can also replicate the error by opening freeview and opening all 
the above files sequentially through the GUI.


Thank you!
Tristan


*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of 
Ruopeng Wang <mailto:rpw...@nmr.mgh..harvard.edu>>

*Sent:*Thursday, August 22, 2019 8:16 AM
*To:*Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*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 <mailto:tpaut...@wisc.edu>> wrote:


External Email - Use Caution
Adding more details provided by my user:

The crash only happens when loading surface files, either via the 
-f flag from the CLI or directly through the GUI. Could this be an 
issue with the surface files or the manner in which they are created?



*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of 
TRISTAN J PAUTSCH <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>

*Sent:*Tuesday, August 20, 2019 2:35 PM
*To:*freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*[Freesurfer] freeview crash -- petsc error when opening 
volume

External Email - Use Caution
Greetings all, I'll try to keep this succinct.

I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here 
at the lab. I used the stable 6..0/CentOS 6 download, in addition 
to the dev version of freeview per the .../fswiki/UpdateFreeview 
instructions. All dependencies have ostensibly been satisfied, all 
libs from 'ldd freeview.bin' installed. Freeview launches fine and 
stays open when launched alone, however attempting to open a 
volume (either through the GUI or directly via the CLI) causes a 
crash a

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

[Ruopeng Wang]

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 lh.orig:overlay=lh.thickness:overlay_color=colorwheel

Best,
Ruopeng

On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:


External Email - Use Caution

Hi Doug and Roupeng,
did you already have the chance to look into the question how to 
display the color wheel with rtview and/or freeview?

Thank you! Caspar

Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik 
>:


External Email - Use Caution

Hi Doug and Ruopeng,
it would be amazing if you could dig out the information on how to
display the color wheel.
Looking forward to what you find!
Caspar


Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:

Hi Caspar, sorry for the delay. I have not used the retinotoy
stream in a long, long time so I don't know off the top of my
head. I'll have to look into it. tksurfer (from rtview) does
have a way to display using the color wheel, but I don't
remember how to do it.

Ruopeng, can freeview display using a color wheel?

On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:


External Email - Use Caution

Hi!
I wanted to ask again whether there is a way to display the
color wheel in rtview and/or freeview. We are debugging our
analyses and it would be immensely helpful to have a legend
that specifies the color assignments.
Thank you,
Caspar

On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
mailto:cschwie...@rockefeller.edu>> wrote:

Hi!
I am following up on this thread trying to understand how
to make the color wheel visible in rtview, or, if
necessary, in freeview.
Thank you! Caspar


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

[Ruopeng Wang]

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 FreeView 
Version 2.0 Builed Jan 18 2017 16:48:55.


I've searched the list and the wiki and I didn't find a similar 
information.

Thanks :) Regards,
Ysr H




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

[Ruopeng Wang]

You can tell the order from the orientation string. For example PIL means 
coronal (P-A), axial(I-S) and sagittal (L-R).

Ruopeng

> On Aug 29, 2019, at 12:12 PM, Hoke, Harris  wrote:
> 
> I just needed to modify the last set of coordinates for sagittal, and the 
> first for coronal.
> 
> How can I tell which coordinate I should modify -- is it the Primary Slice 
> Direction or the PIL orientation?
> 
> freeview -v SUB/mri/orig/001.mgz -layout 1 -cc -nocursor
> 
> -viewport sagittal -slice 127 127 80 -ss  ~/snaps/T1_sag_1.jpg -noquit 
> -viewport sagittal -slice 127 127 90 -ss  ~/snaps/T1_sag_2.jpg -noquit 
> 
> -viewport axial -slice 127 80 127 -ss  ~/snaps/T1_ax_1.jpg -noquit 
> -viewport axial -slice 127 90 127 -ss  ~/snaps/T1_ax_2.jpg -noquit 
> 
> -viewport coronal -slice 80 127 127 -ss  ~/snaps/T1_cor_1.jpg -noquit 
> -viewport coronal -slice 90 127 127 -ss  ~/snaps/T1_cor_2.jpg -noquit 
> 
> -quit
> 
> On Thu, Aug 29, 2019 at 10:45 AM Hoke, Harris  <mailto:hh...@g.harvard.edu>> wrote:
> Fixed, thank you so much!
> 
> Here's that output:
>   type: MGH
> dimensions: 240 x 256 x 192
>voxel sizes: 1.00, 1.00, 1.00
>   type: SHORT (4)
>fov: 256.000
>dof: 0
> xstart: -120.0, xend: 120.0
> ystart: -128.0, yend: 128.0
> zstart: -96.0, zend: 96.0
> TR: 2300.00 msec, TE: 2.96 msec, TI: 900.00 msec, flip angle: 
> 9.00 degrees
>nframes: 1
>PhEncDir: ROW
>FieldStrength: 3.00
> ras xform present
> xform info: x_r =   0.0468, y_r =  -0.0119, z_r =  -0.9988, c_r =
> -0.0820
>   : x_a =  -0.9976, y_a =   0.0510, z_a =  -0.0474, c_a =
> 10.6233
>   : x_s =  -0.0515, y_s =  -0.9986, z_s =   0.0095, c_s =
> 20.6047
> 
> talairach xfm : 
> Orientation   : PIL
> Primary Slice Direction: sagittal
> 
> voxel to ras transform:
> 0.0468  -0.0119  -0.998891.7159
>-0.9976   0.0510  -0.0474   128.3579
>-0.0515  -0.9986   0.0095   153.6901
> 0.   0.   0. 1.
> 
> voxel-to-ras determinant -1
> 
> ras to voxel transform:
> 0.0468  -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.edu>> wrote:
> 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 28, 2019, at 7:21 PM, Hoke, Harris  <mailto:hh...@g.harvard.edu>> wrote:
> 
>> correction:
>> the output of uname -a should be 
>> Linux ncfood02.rc.fas.harvard.edu <http://ncfood02.rc.fas.harvard.edu/> 
>> 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 29 14:59:59 UTC 2019 x86_64 x86_64 
>> x86_64 GNU/Linux
>> Sorry for the confusion.
>> 
>> 
>> On Wed, Aug 28, 2019 at 7:18 PM Hoke, Harris > <mailto:hh...@g.harvard.edu>> wrote:
>> Freeview does not update in the viewer window to the correct slice position 
>> when calling on viewport. This means instead of taking snapshots of N slices 
>> of the brain from N specified slice coordinates, it takes the same snapshot 
>> over and over again.
>> Originally, we found a workaround by disabling qt_setup in the freeview tcsh 
>> script:
>> #source $FREESURFER_HOME/bin/qt_setup. 
>> After this, it worked perfectly. Since then, it has stopped working well. 
>> 
>> The error occurs for saggital and coronal views. (Axial works fine, for some 
>> reason). I am using the stable release of freesurfer 6.0.0. The problem 
>> still happens if I interleave axial/coronal/saggital viewport commands, 
>> instead of running them together as below. The problem also occurs using the 
>> development version of freesurfer from august 27th, CentOS7 build (but only 
>> for sagittal and coronal; Axial works fine).
>> 
>> freeview -cmd minimalcmd.txt
>> 
>> minimalcmd.txt:
>> freeview -v SUBDIR/mri/orig/001.mgz -layout 1 -cc -nocursor
>> 
>> -viewport sagittal -slice 80 127 127 -ss  OUTDIR/T1_sag_1.jpg -noquit 
>> -viewport sagittal -slice 90 127 127 -ss  OUTDIR/T1_sag_2.jpg -noquit 
>> 
>> -viewport axial -slice 127 80 127 -ss  OUTDIR/T1_ax_1.jpg -noquit 

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

[Ruopeng Wang]

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 28, 2019, at 7:21 PM, Hoke, Harris  wrote:
> 
> correction:
> the output of uname -a should be 
> Linux ncfood02.rc.fas.harvard.edu 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 
> 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
> Sorry for the confusion.
> 
> 
>> On Wed, Aug 28, 2019 at 7:18 PM Hoke, Harris  wrote:
>> Freeview does not update in the viewer window to the correct slice position 
>> when calling on viewport. This means instead of taking snapshots of N slices 
>> of the brain from N specified slice coordinates, it takes the same snapshot 
>> over and over again.
>> Originally, we found a workaround by disabling qt_setup in the freeview tcsh 
>> script:
>> #source $FREESURFER_HOME/bin/qt_setup. 
>> After this, it worked perfectly. Since then, it has stopped working well. 
>> 
>> The error occurs for saggital and coronal views. (Axial works fine, for some 
>> reason). I am using the stable release of freesurfer 6.0.0. The problem 
>> still happens if I interleave axial/coronal/saggital viewport commands, 
>> instead of running them together as below. The problem also occurs using the 
>> development version of freesurfer from august 27th, CentOS7 build (but only 
>> for sagittal and coronal; Axial works fine).
>> 
>> freeview -cmd minimalcmd.txt
>> 
>> minimalcmd.txt:
>> freeview -v SUBDIR/mri/orig/001.mgz -layout 1 -cc -nocursor
>> 
>> -viewport sagittal -slice 80 127 127 -ss  OUTDIR/T1_sag_1.jpg -noquit 
>> -viewport sagittal -slice 90 127 127 -ss  OUTDIR/T1_sag_2.jpg -noquit 
>> 
>> -viewport axial -slice 127 80 127 -ss  OUTDIR/T1_ax_1.jpg -noquit 
>> -viewport axial -slice 127 90 127 -ss  OUTDIR/T1_ax_2.jpg -noquit 
>> 
>> -viewport coronal -slice 127 127 80 -ss  OUTDIR/T1_cor_1.jpg -noquit 
>> -viewport coronal -slice 127 127 90 -ss  OUTDIR/T1_cor_2.jpg -noquit 
>> 
>> -quit
>> 
>> In case it's useful:
>> uname -a
>> Linux ncfservice02 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 
>> 2018 x86_64 x86_64 x86_64 GNU/Linux
>> 
>> I'm unsure what else I can try or what other information I can provide. 
>> Please let me know.
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Re: [Freesurfer] trouble with freeview View > Show Color Scale

[Ruopeng Wang]

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 
> TRACULA and have loaded a text file containing p-values from an analysis 
> (Spline Color: Heatscale, Scalar map: my p-values file). The values display 
> correctly on the tract.
> 
> However, when I use View > Show Color Scale, it looks like the color scale is 
> generated is for the black-and-white volume, instead of for those values. See 
> attached screenshot. I'm instead trying to generate a Color Scale at the 
> right of the figure that shows which colors (yellow to red) correspond to 
> which p-values. 
> 
> Thanks for your help,
> Liz
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

[Ruopeng Wang]

Hi Tristan,

Thanks for the files. I have no problem loading them with the latest dev build 
and stable 6.0 build. I do not have an Ubuntu system, though. 

If I’m not mistaken you use dev version of freeview binary along with stable 
6.0 FS binary. Is that correct? Is there any chance you can try installing the 
whole FS dev package?

Ruopeng

> On Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH  wrote:
> 
> External Email - Use Caution
> Ruopeng,
> 
> I've uploaded the files to the FTP drop 
> (transfer/incoming/freesurfer_data.tar.gz). The command my user is running 
> against these files is:
> 
> freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow 
> lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magenta
> 
> We can also replicate the error by opening freeview and opening all the above 
> files 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 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 > <mailto:tpaut...@wisc.edu>> wrote:
>> 
>> External Email - Use Caution
>> Adding more details provided by my user:
>> 
>> The crash only happens when loading surface files, either via the -f flag 
>> from the CLI or directly through the GUI. Could this be an issue with the 
>> surface files or the manner in which they are created?
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of TRISTAN J 
>> PAUTSCH > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>> Sent: Tuesday, August 20, 2019 2:35 PM
>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
>> mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: [Freesurfer] freeview crash -- petsc error when opening volume
>>  
>> External Email - Use Caution
>> Greetings all, I'll try to keep this succinct. 
>> 
>> I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. 
>> I used the stable 6.0/CentOS 6 download, in addition to the dev version of 
>> freeview per the .../fswiki/UpdateFreeview instructions. All dependencies 
>> have ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. 
>> Freeview launches fine and stays open when launched alone, however 
>> attempting to open a volume (either through the GUI or directly via the CLI) 
>> causes a crash and the following error about 5-8 seconds after launching 
>> (brain images begin to populate, then crash):
>> 
>> ---
>> 
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see 
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>>  
>> <http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC>
>>  ERROR: or try http://valgrind.org <http://valgrind.org/> on linux or man 
>> libgmalloc on Apple to find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
>> run 
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: - Error Message 
>> 
>> [0]PETSC ERROR: Signal received!
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
>> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Unknown Name on a linux-gnu named xxx by xxx Tue Aug 
>> 20 13:44:15 2019
>> [0]PETSC ERROR: Librarie

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

[Ruopeng Wang]

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 surface files, either via the -f flag 
> from the CLI or directly through the GUI. Could this be an issue with the 
> surface files or the manner in which they are created?
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of TRISTAN J PAUTSCH 
> 
> Sent: Tuesday, August 20, 2019 2:35 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: [Freesurfer] freeview crash -- petsc error when opening volume
>  
> External Email - Use Caution
> Greetings all, I'll try to keep this succinct. 
> 
> I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. 
> I used the stable 6.0/CentOS 6 download, in addition to the dev version of 
> freeview per the .../fswiki/UpdateFreeview instructions. All dependencies 
> have ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. 
> Freeview launches fine and stays open when launched alone, however attempting 
> to open a volume (either through the GUI or directly via the CLI) causes a 
> crash and the following error about 5-8 seconds after launching (brain images 
> begin to populate, then crash):
> 
> ---
> 
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>  ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to 
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
> run 
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named xxx by xxx Tue Aug 
> 20 13:44:15 2019
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> Segmentation fault (core dumped)
> 
> ---
> 
> I've seen a number of other posts on the mailing list about this, but all of 
> them I could find either end abruptly without a solution or with an 
> unanswered request for more info. 
> 
> Happy to provide any additional information or anything that may aid in the 
> resolution of this issue. 
> 
> Thanks everyone,
> ~T
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Re: [Freesurfer] spatial scale bar question

[Ruopeng Wang]

The 3D scale is also a 3d object in the view. When you zoom the view, the scale 
will also zoom. But the number should not change. 

> On Aug 16, 2019, at 10:25 AM, Nasiriavanaki, Zahra 
>  wrote:
> 
> Hi Ruopeng
> 
> Thanks for your reply.
> I have a question though. When I zoom in the 3D image, the scale bar numbers 
> don't change. Shouldn't they change when I zoom in?
> 
> Thanks 
> Mona
> 
> Zahra (Mona) Nasiriavanaki
> Postdoctoral Research Fellow
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 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
>  
> 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 
>> mailto:znasiriavan...@mgh.harvard.edu>> 
>> wrote:
>> 
>> Hi Freesurfer experts
>> 
>> I wanted to follow up on my question about "spatial scale bar" for 
>> significancy maps in FS.
>> I appreciate if you let me know about the updates on that.
>> 
>> Thanks
>> Mona
>> 
>> Zahra (Mona) Nasiriavanaki
>> Postdoctoral Research Fellow
>> Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> 149 13th Street, 149-2615
>> Charlestown, MA, USA, 02129
>> 
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Bruce Fischl 
>> mailto:fis...@nmr.mgh.harvard.edu>>
>> Sent: Monday, May 13, 2019 9:56:41 AM
>> To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: Re: [Freesurfer] spatial scale bar question
>>  
>> Hi Mona
>> 
>> sure. As I said it is a bit more complicated than it seems. Ruopeng will 
>> post a note when something usable is in the dev version
>> 
>> Bruce
>> 
>> 
>> On Mon, 13 May 
>> 2019, Nasiriavanaki, Zahra wrote:
>> 
>> > 
>> > Yes Bruce.
>> > 
>> > It doesn't work.
>> > 
>> > I appreciate if you could let me know when you had any updates on it.
>> > 
>> > 
>> > Thanks
>> > 
>> > Mona
>> > 
>> > ___
>> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>> > > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of
>> > Bruce Fischl > > <mailto:fis...@nmr.mgh.harvard.edu>>
>> > Sent: Friday, May 10, 2019 6:15:05 PM
>> > To: Freesurfer support list
>> > Subject: Re: [Freesurfer] spatial scale bar question  
>> > I don't think it currently works in 3D mode as it is not trivial due to
>> > perspective transforms. Ruopeng is trying some things
>> > On Fri, 10 May 2019,
>> > Greve, Douglas N.,Ph.D. wrote:
>> > 
>> > > here is a pick of it
>> > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif 
>> > > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif>
>> > 
>> > [fv.colorbar.gif]
>> > 
>> > 
>> > >
>> > >
>> > > On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
>> > >
>> > >   Thanks for your reply.
>> > >
>> > >   I have overlaid the significance map on an inflated brain, and I 
>> > > don't see the scale
>> > >   bar icon anywhere.
>> > >
>> > >   tksurferfv fsaverage lh inflated -ov sig.nii.gz
>> > >
>> > >
>> > >__
>> > _
>> > > From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>> > > > > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on
>> > > behalf of Greve, Douglas N.,Ph.D. > > > <mailto:dgr...@mgh.harvard.edu>&g

Re: [Freesurfer] spatial scale bar question

[Ruopeng Wang]

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 to follow up on my question about "spatial scale bar" for 
> significancy maps in FS.
> I appreciate if you let me know about the updates on that.
> 
> Thanks
> Mona
> 
> Zahra (Mona) Nasiriavanaki
> Postdoctoral Research Fellow
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street, 149-2615
> Charlestown, MA, USA, 02129
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: Monday, May 13, 2019 9:56:41 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] spatial scale bar question
>  
> Hi Mona
> 
> sure. As I said it is a bit more complicated than it seems. Ruopeng will 
> post a note when something usable is in the dev version
> 
> Bruce
> 
> 
> On Mon, 13 May 
> 2019, Nasiriavanaki, Zahra wrote:
> 
> > 
> > Yes Bruce.
> > 
> > It doesn't work.
> > 
> > I appreciate if you could let me know when you had any updates on it.
> > 
> > 
> > Thanks
> > 
> > Mona
> > 
> > ___
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  on behalf of
> > Bruce Fischl 
> > Sent: Friday, May 10, 2019 6:15:05 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] spatial scale bar question  
> > I don't think it currently works in 3D mode as it is not trivial due to
> > perspective transforms. Ruopeng is trying some things
> > On Fri, 10 May 2019,
> > Greve, Douglas N.,Ph.D. wrote:
> > 
> > > here is a pick of it
> > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif 
> > > 
> > 
> > [fv.colorbar.gif]
> > 
> > 
> > >
> > >
> > > On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
> > >
> > >   Thanks for your reply.
> > >
> > >   I have overlaid the significance map on an inflated brain, and I 
> > > don't see the scale
> > >   bar icon anywhere.
> > >
> > >   tksurferfv fsaverage lh inflated -ov sig.nii.gz
> > >
> > >
> > >__
> > _
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> > >  on
> > > behalf of Greve, Douglas N.,Ph.D. 
> > > Sent: Friday, May 10, 2019 3:27:15 PM
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] spatial scale bar question  
> > > In freeview, it is just an icon above the image window. Click on it and 
> > > it should give you a
> > > scale bar
> > >
> > > On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
> > >
> > >   Dear Freesurfers 
> > >
> > >   Hi
> > >
> > >
> > >   I am trying to add a spatial scale bar to my cortical maps in 
> > > tksurfer. However,
> > >   as it's mentioned in Freesurfer forum before, the scale bar in 
> > > tksurfer shrinks
> > >   when you zoom in the brain.
> > >
> > >   I couldn't find a scale bar option in Freeview neither.
> > >
> > >   I appreciate if you could let me know how to get a scale bar.
> > >
> > >
> > >   Thanks
> > >
> > >   Mona
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > > 
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > > 
> > >
> > >
> > >
> > >
> > 
> >
> ___
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Re: [Freesurfer] Error opening Freeview

[Ruopeng Wang]

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 Freeview (The most recent version): it loads 
.mgz and labels correctly, but then after 5 seconds it shuts off, 
giving off this error:




qt_xcb_createCursorXRender: query_pict_formats failed
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
probably memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC 
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple 
to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, 
and run

[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 


[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 
17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named beta by nick Mon Jul 
 1 16:25:24 2019
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt

[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 
--with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 
COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory 
unknown file

[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault

​
I was wondering if there's anything I can do to debug, or whether it's 
just a lack of computer capacity on our end.


Best,


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
ph: 617 754 1237
--



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Re: [Freesurfer] TrackVis question

[Ruopeng Wang]

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. 
> This data is from 7T scanners. I used an Angle threshold of 50. I tried 
> various gradients from 6 - 120, but the images I am getting on trackvis are 
> weird. I have attached a screenshot.
> 
> Can you please shed some light on this?
> 
> Thank you,
> 
> Alan
> 
> 
> -- 
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> 
> Alan N. Francis PhD
> Instructor in Psychiatry
> Harvard Medical School
> 
> Louis V. Gerstner III scholar
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149, 13th street, Charlestown, MA
> al...@bwh.harvard.edu  
> afran...@mclean.harvard.edu 
>   
>  
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Re: [Freesurfer] Fwd: Visualizing Volumetric Files on Surface

[Ruopeng Wang]

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: "freesurfer@nmr.mgh.harvard.edu" 
>> Date: Thu, 09 May 2019 01:24:58 +0430
>> Subject: Visualizing Volumetric Files on Surface
>> Dear FreeSurfer experts;
>> I have created some volumetric(.nii) files in FreeSurfer (the procedure
>> is
>> as following: lh/rh.aparc.annot> mri_divide_parcellation >
>> mri_aparc2aseg >
>> deleting subcortical and white matter regions in order to keep just
>> cortical
>> regions on GM).
>>
>> Now I wanna visualize my volumetric files on surface so that I myself
>> can
>> determine the color of each region. But I dunno how to do it exactly.
>>   I would be grateful if u could help me with that.
>> Thanks in advance
>> Best regards
>> Maedeh,
>>
>>
>
>
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Re: [Freesurfer] Color scale error

[Ruopeng Wang]

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 problems loading a colorbar. I am trying to 
> run this code: freeview -f 
> /data/sugrue2/ABCD/fsaverage/surf/rh.pial:overlay=/data/sugrue2/ABCD/temp/testing.mgh:overlay_threshold=0,1:overlay_method=linear
>  -viewport 3d -hide-3d-slices -nocursor —colorscale. The resulting color 
> scale makes no sense in that it does not properly display the min and max 
> values specified. As you can see in the screenshot, the color scale runs from 
> 1e-10 to -1e-10. Configuring the colors from the GUI seems to fix the issue, 
> but Ideally I would like to automate the screenshot process.
> 
> Any help is greatly appreciated.
> 
> 
> 
> Ryan Michael Nillo
> Staff Research Associate I
> University of California San Francisco
> Department of Radiology and Biomedical Imaging
> 
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Re: [Freesurfer] freeview and complex values

[Ruopeng Wang]

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 (real and imag) values
> generated by a retinotopy analysis in a 'color wheel' format (similar
> to what tksurfer does).
>
> Any hint?
>
>
> _
>
> Shahin Nasr
>
> Assistant Prof. in Radiology
> Harvard Medical School
> Martinos Imaging Center, MGH
> Bldg 149, 13th street,
> Charlestown, MA 02129
>
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Re: [Freesurfer] Custom Colormap

[Ruopeng Wang]

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 11:34 AM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


I see. You can give freeview a custom lookup table on the command line

cheers
Bruce


On Mon, 1 Apr 2019, Emanuel Alvaredo wrote:

>
> External Email - Use Caution
>
> Thanks for the answer Bruce.
> Is For segmentations. I have run freesurfer for 100 nomal
patients. I have calculated
> standard desviation and mean, then I am comparing the results
against a patological
> patient. So, I would like to open freeview, for example with
this command
>
> freeview -v mri/orig.mgz -f  surf/lh.white:edgecolor=blue
surf/lh.pial:edgecolor=red
> surf/rh.white:edgecolor=blue
> surf/rh.pial:edgecolor=red
>

surf/rh.inflated:overlay=surf/rh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwhe
>

el,inverse:overlay=surf/rh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse:
>

overlay=surf/rh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse

>

surf/lh.inflated:overlay=surf/lh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwhe
>

el,inverse:overlay=surf/lh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse:
>

overlay=surf/lh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse
>
> and show in my custom colores in segments.
>
>
>
>
> Emanuel
>
>
> On Mon, Apr 1, 2019 at 11:17 AM Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>
wrote:
>       Hi Emanuel
>
>       can you tell us more. For parellations or segmentations?
Are you just
>       changing the color of existing parcels/segments? If so you
can just
>       import it in freeview
>       cheers
>       Bruce
>
>       On Mon, 1 Apr 2019, Emanuel Alvaredo wrote:
>
>       >
>       > External Email - Use Caution
>       >
>       > Hello!
>       > I would like to ask you  about customs colormaps. I have
created my
>       > own FreeSurferColorLUT.txt and I  would like configure
the color map using
>       command line.
>       > Is it possible?
>       >
>       > Thanks in advance.
>       >
>       > Emanuel
>       >
>       >___
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>
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Re: [Freesurfer] [how to highlight a known ROI in original MR Image]

[Ruopeng Wang]

Every item in the color table should be checkable. You can uncheck all and then 
check the one you want to show.

> On Mar 20, 2019, at 4:46 PM, Yi Li  wrote:
> 
> External Email - Use Caution
> 
> Hi Ruopeng,
> 
> I have updated freeview. Which options to use?
> 
> 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 update 
>> your freeview:
>> 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
>> 
>> Best,
>> Ruopeng
>> 
>>> On 3/20/19 3:20 PM, Yi Li wrote:
>>> External Email - Use Caution
>>> 
>>> Hi,
>>> 
>>>  
>>> 
>>> I want to highlight one known ROI (eg left caudate) in a MR image. I 
>>> understand known ROIs are already in aseg or aparc and there is a color 
>>> look up table, but I want to highlight one ROI at a time.
>>> 
>>>  
>>> 
>>> I searched the website, and found the following instructions, but it 
>>> highlighted the region of lh.BA45 which has label file at 
>>> $sub/label/lh.BA45.label. I couldn’t find label file at 
>>> $sub/label/lh.caudate.label. Is there any way to get a known ROI to be 
>>> highlighted as in the fig below?  Thank you so much for the help.
>>> 
>>>  
>>> 
>>> Best Regards
>>> 
>>> Yi
>>> 
>>>  
>>> 
>>> 
>>> 
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
>>> 
>>>  
>>> 
>>> cd $SUBJECTS_DIR
>>> 
>>> mri_label2label \
>>> 
>>>   --srcsubject fsaverage \
>>> 
>>>   --srclabel fsaverage/label/lh.BA45.label \
>>> 
>>>   --trgsubject 004 \
>>> 
>>>   --trglabel 004/label/lh.BA45.label \
>>> 
>>>   --hemi lh \
>>> 
>>>   --regmethod surface
>>> 
>>>  
>>> 
>>> freeview -v 004/mri/orig.mgz
>>> 
>>>  
>>> 
>>> Then on the menu bar click File > Load ROI  choose 
>>> lh.BA45.label and hit 'Open'. The label is visible in coronal slice 153. To 
>>> jump to that slice, double click on the coordinates [127,127,128] next to 
>>> where it says 'orig' in the Cursor window pane. The last number is the 
>>> slice number. Change it to 153 and hit enter. 
>>> 
>>>  
>>> 
>>> 
>>> 
>>>  
>>> 
>>> ---
>>> 
>>> The information in this email, including attachments, may be confidential 
>>> and is intended solely for the addressee(s). If you believe you received 
>>> this email by mistake, please notify the sender by return email as soon as 
>>> possible. 
>>> 
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> ---
> 
> The information in this email, including attachments, may be confidential and 
> is intended solely for the addressee(s). If you believe you received this 
> email by mistake, please notify the sender by return email as soon as 
> possible.
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Re: [Freesurfer] [how to highlight a known ROI in original MR Image]

[Ruopeng Wang]

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:


External Email - Use Caution

Hi,

I want to highlight one known ROI (eg left caudate) in a MR image. I 
understand known ROIs are already in aseg or aparc and there is a 
color look up table, but I want to highlight one ROI at a time.


I searched the website, and found the following instructions, but it 
highlighted the region of lh.BA45 which has label file at 
$sub/label/lh.BA45.label. I couldn’t find label file at 
$sub/label/lh.caudate.label. Is there any way to get a known ROI to be 
highlighted as in the fig below?  Thank you so much for the help.


Best Regards

Yi



https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

cd $SUBJECTS_DIR

mri_label2label \

  --srcsubject fsaverage \

  --srclabel fsaverage/label/lh.BA45.label \

  --trgsubject 004 \

  --trglabel 004/label/lh.BA45.label \

  --hemi lh \

  --regmethod surface

freeview -v 004/mri/orig.mgz

Then on the menu bar click *File > Load ROI loadroi.jpeg 
*choose* lh.BA45.label* and hit 'Open'. The label is visible in 
coronal slice 153. To jump to that slice, double click on the 
coordinates [127,127,128] next to where it says 'orig' in the Cursor 
window pane. The last number is the slice number. Change it to 153 and 
hit enter.


---

The information in this email, including attachments, may be 
confidential and is intended solely for the addressee(s). If you 
believe you received this email by mistake, please notify the sender 
by return email as soon as possible.


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Re: [Freesurfer] problems with Freeview

[Ruopeng Wang]

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...@nmr.mgh.harvard.edu>>) 
escribió:


Can you send us a T1.mgz file along with a lh.white file that do
not align when loaded in freeview?

On 1/31/19 10:47 AM, Laboratorio de Neurociencia Funcional wrote:

No, we didn't have the same problem neither with Freesurfer 6.0
or with the development Freesurfer version. The problem only
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...@nmr.mgh.harvard.edu>>) escribió:

That’s unlikely. Did FS 6.0 have the same problem?


On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia
Funcional mailto:neuroaging...@gmail.com>> wrote:

External Email - Use Caution


Hi Ruopeng,

we have tried these commands with Bert and with different
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 Wang
(mailto:rpw...@nmr.mgh.harvard.edu>>) escribió:

Your screenshot appears to be from burt data but I
assume it was loaded with similar commands. I could not
replicate the displacement with burt data. Would it be
possible to send me T1.mgz and lh.white file from this
OSM_0 subject?

Thanks,
Ruopeng



On Jan 31, 2019, at 9:18 AM, Laboratorio de
Neurociencia Funcional mailto:neuroaging...@gmail.com>> wrote:

External Email - Use Caution


Sure, commands are copied below:

*File > Run Command*

*-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz*

*-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz*

*-**f
/usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow*

*-f
/usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red*

*-f
/usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow*

*-f
/usr/local/freesurfer/subjects/OSM_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?

Ruopeng


On Jan 31, 2019, at 7:31 AM, Laboratorio de
Neurociencia Funcional mailto:neuroaging...@gmail.com>> wrote:

External Email - Use Caution


Dear Freesurfers,

we have installed the updated Freeview version in
the development version of Freesurfer (Centos 6,
18 january build), but Bert images appear
displaced when they are loaded with this version
of Freeview. The same displacement occurs when
other dataset is used. Please find attached a
screenshot to display the issue. Would you please
help me to solve the problem?

Thank you in advance.

Best,
Jose
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Re: [Freesurfer] problems with Freeview

[Ruopeng Wang]

Can you send us a T1.mgz file along with a lh.white file that do not 
align when loaded in freeview?


On 1/31/19 10:47 AM, Laboratorio de Neurociencia Funcional wrote:
No, we didn't have the same problem neither with Freesurfer 6.0 or 
with the development Freesurfer version. The problem only 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...@nmr.mgh.harvard.edu>>) 
escribió:


That’s unlikely. Did FS 6.0 have the same problem?


On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia
Funcional mailto:neuroaging...@gmail.com>> wrote:

External Email - Use Caution


Hi Ruopeng,

we have tried these commands with Bert and with different
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 Wang
(mailto:rpw...@nmr.mgh.harvard.edu>>) escribió:

Your screenshot appears to be from burt data but I assume it
was loaded with similar commands. I could not replicate the
displacement with burt data. Would it be possible to send me
T1.mgz and lh.white file from this OSM_0 subject?

Thanks,
Ruopeng



On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia
Funcional mailto:neuroaging...@gmail.com>> wrote:

External Email - Use Caution


Sure, commands are copied below:

*File > Run Command*

*-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz*

*-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz*

*-**f
/usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow*

*-f
/usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red*

*-f
/usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow*

*-f
/usr/local/freesurfer/subjects/OSM_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?

Ruopeng


On Jan 31, 2019, at 7:31 AM, Laboratorio de
Neurociencia Funcional mailto:neuroaging...@gmail.com>> wrote:

External Email - Use Caution


Dear Freesurfers,

we have installed the updated Freeview version in the
development version of Freesurfer (Centos 6, 18 january
build), but Bert images appear displaced when they are
loaded with this version of Freeview. The same
displacement occurs when other dataset is used. Please
find attached a screenshot to display the issue. Would
you please help me to solve the problem?

Thank you in advance.

Best,
Jose
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Re: [Freesurfer] problems with Freeview

[Ruopeng Wang]

That’s unlikely. Did FS 6.0 have the same problem?

> On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia Funcional 
>  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Ruopeng, 
> 
> we have tried these commands with Bert and with different 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 Wang ( <mailto:rpw...@nmr.mgh.harvard.edu>>) escribió:
> Your screenshot appears to be from burt data but I assume it was loaded with 
> similar commands. I could not replicate the displacement with burt data. 
> Would it be possible to send me T1.mgz and lh.white file from this OSM_0 
> subject?
> 
> Thanks,
> Ruopeng
> 
> 
>> On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional 
>> mailto:neuroaging...@gmail.com>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Sure, commands are copied below:
>> File > Run Command
>> 
>> -v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz
>> 
>> -v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz
>> 
>> -f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow
>> 
>> -f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red
>> 
>> -f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow
>> 
>> -f /usr/local/freesurfer/subjects/OSM_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?
>> 
>> Ruopeng
>> 
>>> On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional 
>>> mailto:neuroaging...@gmail.com>> wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> 
>>> Dear Freesurfers,
>>> 
>>> we have installed the updated Freeview version in the development version 
>>> of Freesurfer (Centos 6, 18 january build), but Bert images appear 
>>> displaced when they are loaded with this version of Freeview. The same 
>>> displacement occurs when other dataset is used. Please find attached a 
>>> screenshot to display the issue. Would you please help me to solve the 
>>> problem?
>>> 
>>> Thank you in advance.
>>> 
>>> Best,
>>> Jose
>>> >> displacement_Freeview.png>___
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Re: [Freesurfer] problems with Freeview

[Ruopeng Wang]

Your screenshot appears to be from burt data but I assume it was loaded with 
similar commands. I could not replicate the displacement with burt data. Would 
it be possible to send me T1.mgz and lh.white file from this OSM_0 subject?

Thanks,
Ruopeng


> On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional 
>  wrote:
> 
> External Email - Use Caution
> 
> 
> Sure, commands are copied below:
> File > Run Command
> 
> -v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz
> 
> -v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz
> 
> -f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow
> 
> -f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red
> 
> -f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow
> 
> -f /usr/local/freesurfer/subjects/OSM_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?
> 
> Ruopeng
> 
>> On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional 
>> mailto:neuroaging...@gmail.com>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Dear Freesurfers,
>> 
>> we have installed the updated Freeview version in the development version of 
>> Freesurfer (Centos 6, 18 january build), but Bert images appear displaced 
>> when they are loaded with this version of Freeview. The same displacement 
>> occurs when other dataset is used. Please find attached a screenshot to 
>> display the issue. Would you please help me to solve the problem?
>> 
>> Thank you in advance.
>> 
>> Best,
>> Jose
>> > displacement_Freeview.png>___
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Re: [Freesurfer] problems with Freeview

[Ruopeng Wang]

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 development version of 
> Freesurfer (Centos 6, 18 january build), but Bert images appear displaced 
> when they are loaded with this version of Freeview. The same displacement 
> occurs when other dataset is used. Please find attached a screenshot to 
> display the issue. Would you please help me to solve the problem?
> 
> Thank you in advance.
> 
> Best,
> Jose
>  displacement_Freeview.png>___
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Re: [Freesurfer] Highlighting single atlas structures in freeview

[Ruopeng Wang]

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 
>  wrote:
> 
> External Email - Use Caution
> 
> 
> Dear all,
> 
> I would like to show several structures from the DKT (or the 
> Desikan-Killiany) atlas alone on a "blank" fsaverage brain, rather than have 
> all structures displayed in different colors (as happens by default). For 
> instance, I'd like to just show "medialorbitofrontal" on its own, then 
> "middletemporal" on its own, etc.
> 
> After I open the parcellation,
> freeview -v /FS/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f 
> /FS/fsaverage/surf/lh.white:annot=aparc.annot
> , I expected to be able to turn each label in the list on and off like a 
> layer, but this does not work.
> <21-01-2019 14.48.54.jpg>
> 
> I hoped I could use Alt+F to hide/show each atlas label at a time (cf 
> freeview tutorial 
> ), 
> but this instead toggles the entire external surface of the brain on and off.
> 
> Can anyone help? Thank you!
> --Francesco
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Re: [Freesurfer] (no subject)

[Ruopeng Wang]

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 labels, just like in tksurfer.

Best,
Ruopeng

On 1/7/19 11:22 AM, Larissa Bechtle wrote:
>  External Email - Use Caution
>
> Hi everybody,
>   
> after finishing my group analysis I am currently trying to run a ROI analysis.
> However I have some problems/general questions.
> I am trying to draw a ROI on fsaverage in order to use the mri_label2label 
> command afterwards.
> I opened Freeview, clicked on "load surface" first and then chose 
> lh.inflated_avg  (fsaverage -> surf) which worked fine but  I cant choose 
> "New ROI" (in order to crate the ROI).
>   
> So is it possible to draw a ROI when focussing only on the surface? And if 
> this is the case why cant I? Did I chose the wrong file?
> I am really thankful for any help!!
>   
> Larissa
>   
>
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Re: [Freesurfer] Freeview Scrolling through slices on a Mac

[Ruopeng Wang]

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, Chris Petty wrote:
>  External Email - Use Caution
>
>
> Maybe I am missing something, but how can I scroll through slices with 
> keyboard or mouse in Freeview on a Mac?
>
> Nothing I’ve tried works thus far.
>
> Any typical key ( cmd, ctrl, shift ) with scroll just zooms.  Up/down moves 
> the image up and down … shift / option / cmd with up / down either zooms or 
> moves up / down.
>
> I’m just trying to add control points and definitely need to scroll through 
> slices without clicking on the image.
>
> Thanks,
> -Chris
>
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Re: [Freesurfer] freeview showing results in a strange manner

[Ruopeng Wang]

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 results of each 
> region to the template with Matlab (file attached here entitled 
> "lh.subj1.mgz"). However, when I try to open it with freeview, the image 
> looks quite strange ('Picture_1') but it works with tksurfer (Picture_2). 
> Does any one know what is wrong with this? Did I plot the result in a wrong 
> way?
> 
> Thanks very much
> Shize
> 
> 
> 
> 
> --
> Shize Jiang
> Fudan University,
> Department of neurosurgery, Huashan Hospital, Shanghai Medical College
> Shanghai,200032,P.R.China
> Mobile: (86)18317079839
> E-Mail: sjian...@fudan.edu.cn 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>  
> ___
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Re: [Freesurfer] automating custom color map

[Ruopeng Wang]

It should be available tomorrow. You can download it from here *tomorrow*:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

The option is 'overlay_custom'. It can be applied like this:

freeview -f 
lh.orig:overlay=overlay_file:overlay_custom=val1,r1,g1,b1,val2,r2,g2,b2,...


val is the value, r,g, b are RGB components of the color for the value.

Cheers,
Ruopeng


On 11/02/2018 02:41 PM, Nillo, Ryan Michael R wrote:


External Email - Use Caution

Thank you so much, Ruopeng. Do you have an estimated timeline for when 
this option might be done?



Ryan


*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 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 
mailto:ryanmichael.ni...@ucsf.edu>> wrote:


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Hi Freesurfer Users,

I used linear regression to map regional beta values on the fsaverage 
surface. I want to use a colormap that goes from blue to gray or gray 
to red (no cyan and yellow). I've been using a custom colormap shown 
in example.tiff. I've been making this by going into freeview and 
adjusting the parameters from the GUI. Is there a way to load this 
and create a snapshot from the command line? I know you can adjust 
certain parameters like overlay threshold and change the colormap, 
but I don't see an option for "custom". The end goal is to make 
multiple regression models and automate the screenshot process.


Best,

Ryan M Nillo
Staff Research Associate I
UCSF Department of Radiology and Biomedical Imaging
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Re: [Freesurfer] automating custom color map

[Ruopeng Wang]

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 used linear regression to map regional beta values on the fsaverage 
> surface. I want to use a colormap that goes from blue to gray or gray to red 
> (no cyan and yellow). I've been using a custom colormap shown in 
> example.tiff. I've been making this by going into freeview and adjusting the 
> parameters from the GUI. Is there a way to load this and create a snapshot 
> from the command line? I know you can adjust certain parameters like overlay 
> threshold and change the colormap, but I don't see an option for "custom". 
> The end goal is to make multiple regression models and automate the 
> screenshot process.
> 
> Best,
> 
> Ryan M Nillo
> Staff Research Associate I
> UCSF Department of Radiology and Biomedical Imaging
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Re: [Freesurfer] Freeview coordinates

[Ruopeng Wang]

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 the tip.
When I run the command on 'lh.white' surface for example, I don't get 
an affine transform but a simpler one:


vox2ras-tk:
-1  0 0  128
 0  0 1 -128
 0 -1 0  128
 0  0 0  1

So when I apply this transform to a pixel position (152, 66, 73) here 
is the result I get:

-152, 73, -66

But the expected result provided in Freeview as TkRegRAS T1 is:
-23.61, -55.02, 61.25

Which obviously involving an affine transform.

Did I miss something?
Thanks

Cheers,
Florent



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

[Ruopeng Wang]

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:


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Hi! I would like from command line to open one surface with multiple 
ovelays. For example, intead of this


..-f surf/lh.inflated:overlay=surf/lh.sulc 
surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5


I would like to do something like that

-f 
surf/lh.inflated:overlay=surf/lh.sulc,overlay=surf/lh.thickness:overlay_threshold=1,5



is this possible?

Thanks!


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

[Ruopeng Wang]

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 the same set of images with Freeview on two 
different computers. One of the computers, load the images correctly 
(see attached image 1). On the other computer the surfaces are shown 
misaligned (see attached image 2). When we try to load surfaces after 
loading a volume the Command Console shows the following error:*"Did 
not find any volume info. Warning: MatrixInverse failed".*This happens 
with all subjects in this computer.


Freesurfer (v6.0) and Freeview are updated correctly. In both 
computers there are Ubuntu 16.04.


Why Freeview didn´t find any volume info in this computer? Can you 
help us to solve this problem?


Thank you.

--
Sofía Rodríguez Peñuela, Técnico de Laboratorio.
Laboratorio de Neurociencia Funcional
Departamento de Fisiología, Anatomía y Biología Celular.
Universidad Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- España -
Movil: 627273085
Email: srod...@upo.es 
http://www.upo.es/neuroaging/es/


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Re: [Freesurfer] Fwd: vertex MNI305

[Ruopeng Wang]

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 
enough so that the vertex number is shown.


Best,
Ruopeng


On 08/21/2018 10:10 AM, Trisanna Sprung-Much wrote:


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Hi there

Doug can you please confirm? Bruce said you would be the best to 
answer and I've got revisions that are due. Please see the image 
attached. In my manuscript I report the x,y,z next to the vertex 
number in Freeview for MNI coordinates (MNI305) of that vertex. These 
only different very slightly from the RAS and SurfaceRAS coordinates 
above the vertex number in the panel but I'd like confirmation I am 
reporting the correct x.y,z.


best
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology



-- Forwarded message -
From: *Trisanna Sprung-Much* >

Date: Thu, Jul 26, 2018 at 7:35 PM
Subject: vertex MNI305
To: Freesurfer support list >



Hi there

This might be a very silly question but I actually cannot find the 
answer in the email archive:


Assuming I have loaded a label onto fsaverage in Freeview and want to 
get the MNI305 coordinate of that labelled vertex, am I simply using 
the x,y,z in brackets in the panel? I attach a photo of what I mean.


Best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology




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

[Ruopeng Wang]

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:


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Dear Freesurfer team,

After loading a volume in Freeview, we try to load surfaces, but 
surfaces are shown misaligned (see attached image) and the Command 
Console shows the following error: "Did not find any volume info. 
Warning: MatrixInverse failed".


This happens with all subjects. If those subjects are open with 
tkmedit, the software does not show any error.


Freesurfer v6.0 and Freeview are updated correctly. We use Ubuntu 16.04.

Can you help us to solve this problem? Do you know the solution?

Thank you

--
Sofía Rodríguez Peñuela, Técnico de Laboratorio.
Laboratorio de Neurociencia Funcional
Departamento de Fisiología, Anatomía y Biología Celular.
Universidad Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- España -
Movil: 627273085
Email: srod...@upo.es 
http://www.upo.es/neuroaging/es/


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Re: [Freesurfer] fthresh function in tksurfer

[Ruopeng Wang]

HI Srishti,

Please download the latest build from here:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview 
<https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview>

Best,
Ruopeng

> On Jul 11, 2018, at 3:49 PM, srishti goel <23srishtig...@gmail.com 
> <mailto:23srishtig...@gmail.com>> wrote:
> 
> Hi Rupoeng,
> 
> Yes it says built in February 2018.
> 
> Could you please tell me once the Mac build of Freeview is updated so I can 
> download the newest version.
> 
> Thank you so much, really appreciate it!
> 
> 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
> 
> 
> On Wed, Jul 11, 2018 at 3:35 PM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> Hi Srishti,
> 
> The mac build of freeview on our download page appears to be quite old. If 
> you go to About menu, you should see the build time. We will update it 
> shortly.
> 
> Best,
> Ruopeng
> 
> On 07/11/2018 03:02 PM, srishti goel wrote:
>> Hi Rupoeng,
>> 
>> I dowloaded the nightly as you had suggested, followed the steps in the link 
>> you had sent but I am still not able to see the z-order function. I tried it 
>> a couple of time, deleting and re-doing everything again but I can't see the 
>> z-order option in Freeview.
>> 
>> Please let me know what else can I do to check that. 
>> 
>> 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
>> 
>> 
>> On Wed, Jul 11, 2018 at 2:59 PM, srishti goel <23srishtig...@gmail.com 
>> <mailto:23srishtig...@gmail.com>> wrote:
>> Hi Rupoeng,
>> 
>> I dowloaded the nightly as you had suggested, followed the steps in the link 
>> you had sent but I am still not able to see the z-order function. I tried it 
>> a couple of time, deleting and re-doing everything again but I can't see the 
>> z-order option in Freeview. I have attached two screenshots of what the 
>> Freeview looks like to me.
>> 
>> Please let me know what else can I do to check that. 
>> 
>> 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
>> 
>> 
>> On Thu, Jul 5, 2018 at 1:43 PM, srishti goel <23srishtig...@gmail.com 
>> <mailto:23srishtig...@gmail.com>> wrote:
>> Thanks so much Ruopeng
>> 
>> 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
>> 
>> 
>> On Thu, Jul 5, 2018 at 1:40 PM, Ruopeng Wang > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>> After you load the label or overlay you should see it on the left panel.
>> 
>> Best,
>> Ruopeng
>> 
>> 
>>> On Jul 5, 2018, at 12:54 PM, srishti goel <23srishtig...@gmail.com 
>>> <mailto:23srishtig...@gmail.com>> wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> 
>>> Hi Rupoeng, 
>>> 
>>> We downloaded the nightly build for that option but I don't see it coming 
>>> on the GUI. I scrolled through every option on the task bar and also the 
>>> left panel on the GUI but nothing corresponded to 'z-order'. Could you 
>>> please direct me to where exactly should I be looking for this option?
>>> 
>>> Thanks,
>>> 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
>>> 
>>> 
>>> On Mon, Jun 11, 2018 at 10:34 AM, Ruopeng Wang >> <mailto:rp

Re: [Freesurfer] Custom color map in Freeview

[Ruopeng Wang]

Hi Ben,

My last email was referring to how to load custom color map for volume 
viewing. If you want to load custom color for surface, you need to 
create and load an RGB map file. The file can be a text file contains N 
lines of RGB color like this:


R1, G1, B1
R2, G2, B2

...

or a volume file with dimension of  N x 3 x1. N must match the number of 
vertices of the surface.


Best,
Ruopeng


On 07/10/2018 04:57 PM, Ben Smith wrote:


External Email - Use Caution

I've been trying to do this as well, but I can't see the right place 
to specify in freesurfer to specify an alternative lookup table.


For instance, if I am coloring a pial surface, then the first 
possibility is to set a Color (where I can "load RGB map"). But I get 
an error "Cannot load RGB" file if I try to use that to load an LUT 
format file. The other option is where it says "heatmap" i can change 
the option to select a custom label, but if I try to enter an LUT file 
into there, freeview crashes (which is fine, I guess that was the 
wrong place).


So can anyone tell me what I'm missing for the place to load the LUT 
file or an alternative colormap?


Thanks for your 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. To create your own look up table, you can refer
to the content of FreeSurferColorLUT.txt file in your freesurfer
installation directory.

Best,
Ruopeng

On 03/27/2018 03:59 PM, Anna Mynick wrote:

Hi all,

I’m wondering whether there’s a way to create a custom color map
in Freeview that would operate as a alternative to the preset
Greyscale, Heatmap, NIH, PET, Jet and GE Color options.

Ideally, I could assign each number value a given color, e.g.
every “0” value in an .nii file is black, every “1” value is red,
every “2” value is blue, every “3" is green and so on. I already
have the RGB values worked out for each number value; I just need
to know how to format this information and where to put it so
that I can my custom colormap as an option in Freeview.

For my purposes, there would be no need to adjust the assigned
colors based on the overall range of values. For instance, there
would be no need to assign a different color value to a “1” value
depending on whether the highest value in the overall .nii file
is 1 or 100.

I did try reading the related conversation here

<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051277.html> 
but
I can’t seem to find the file it references,
annotval2surfoverlay.m, in the Freesurfer directory.

Thanks very much for your help!
Anna



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Re: [Freesurfer] changing label outlines in tksurfer

[Ruopeng Wang]

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,
> 
> thanks for your quick response! I managed to do most of what I wanted in 
> freeview. My last question: Is there any possibility to increase the 
> thickness of the label outlines? Here the new code:
> freeview -f 
> ${case_dir}/surf/rh.inflated:curvature_method=binary:label=${case_dir}/extracted_label/rh.label1.label:label_color=yellow:label_outline=yes:label=${case_dir}/extracted_label/rh.label2.label:label_color=Cyan:label_outline=yes:overlay=${base_dir}/sig.nii.gz
>  -viewport 3d
> 
> Thanks again,
> Martin
> 
> 
> 
> 
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
> Gesendet: Sonntag, 8. Juli 2018 17:49
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] changing label outlines in tksurfer
> 
> Hi Martin
> 
> can you try freeview instead? We don't support tksurfer anymore, and changing 
> label color/outline color is trivial using freeview.
> 
> cheers
> Bruce
> 
> 
> On
> Sun, 8 Jul 2018, Loeffler, Martin wrote:
> 
>> 
>> External Email - Use Caution
>> 
>> Dear experts,
>> 
>>  
>> 
>> I’m visualizing a 1st level sig-map together with two specific label 
>> files using tksurfer (Freesurfer version 6.0). I’ve extracted those labels 
>> before using mri_annotation2label.
>> 
>> I would like to change the colours of the label outlines. This is 
>> probably a very simple thing to do, but I am somehow stuck and would 
>> appreciate any help.
>> 
>> Here my code:
>> 
>>  
>> 
>> tksurfer Case01 lh inflated \
>> 
>> -tcl my_script.tcl \
>> 
>> -label-outline \
>> 
>> -label ${label_dir}/lh.label1.label\
>> 
>> -label ${label_dir}/lh.label2.label\
>> 
>> -o ${contrast_dir}/contrast1l/sig.nii.gz
>> 
>>  
>> 
>> with the .tcl file containing the following:
>> 
>> labl_set_color 0 0 0 255
>> 
>> labl_set_color 1 0 255 255
>> 
>> make_lateral_view
>> 
>> rotate_brain_x -30
>> 
>> redraw
>> 
>>  
>> 
>> Thanks for your help!
>> 
>> Martin
>> 
>> 
>> 
> 
> ___
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> 


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Re: [Freesurfer] fthresh function in tksurfer

[Ruopeng Wang]

After you load the label or overlay you should see it on the left panel.

Best,
Ruopeng

> On Jul 5, 2018, at 12:54 PM, srishti goel <23srishtig...@gmail.com> wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Rupoeng, 
> 
> We downloaded the nightly build for that option but I don't see it coming on 
> the GUI. I scrolled through every option on the task bar and also the left 
> panel on the GUI but nothing corresponded to 'z-order'. Could you please 
> direct me to where exactly should I be looking for this option?
> 
> Thanks,
> 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
> 
> 
> On Mon, Jun 11, 2018 at 10:34 AM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> Yes, I have put an option called z-order in the GUI to control order of 
> rendering for overlays, labels and annoations. To use it you will need to 
> download and install the nightly build from here:
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview 
> <https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview>
> 
> Best,
> Ruopeng
> 
> 
>> On Jun 9, 2018, at 11:04 AM, srishti goel <23srishtig...@gmail.com 
>> <mailto:23srishtig...@gmail.com>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Hi Ruopeng,
>> 
>> I just wanted to check and see if there is any update about adding the 
>> option of changing surface labels to come below overlays in Freeview.
>> Thanks!
>> 
>> 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
>> 
>> 
>> On Tue, May 29, 2018 at 2:40 PM, srishti goel <23srishtig...@gmail.com 
>> <mailto:23srishtig...@gmail.com>> wrote:
>> Thanks a lot Ruopeng, really appreciate it.
>> 
>> 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
>> 
>> 
>> On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>> It will be added very soon. I'll let you know when it is ready.
>> 
>> Best,
>> Ruopeng
>> 
>> On 05/28/2018 05:35 PM, srishti goel wrote:
>>> Hi Ruopeng,
>>> 
>>> Thank you so much! That option will be super helpful. Are you planning to 
>>> add that option to Freeview soon?
>>> 
>>> 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
>>> 
>>> 
>>> On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang >> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>>> Hi Srishti,
>>> 
>>> In freeview surface labels are always displayed on top of overlays. I will 
>>> add an option to change that.
>>> 
>>> Best,
>>> Ruopeng
>>> 
>>> 
>>>> On May 28, 2018, at 9:18 AM, srishti goel <23srishtig...@gmail.com 
>>>> <mailto:23srishtig...@gmail.com>> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> I did use Freeview but I think using either TkSurfer or Freeview won't 
>>>> matter because what I am trying to figure out is what the fthresh value 
>>>> means for the map.
>>>> From reading the archive, I understand that, for instance, fthresh value 
>>>> of 0.3 will mean that the overlay displays 50% (1/10^3) threshold based on 
>>>> intensity/ only voxels which are overlaid by 50% of the subjects. In my 
>>>> case, the maps are visible at fthresh 0.1 and below but since these are 
>>>> already thresholded maps from a meta-analysis I am not very clear on how 
>>>> to interpret the fthresh here. Is it v

Re: [Freesurfer] Freeview not showing images

[Ruopeng Wang]

What if you run 'glxgears'? Does it render properly?

Ruopeng


On 06/29/2018 09:50 AM, Mark Wagshul wrote:


Yes, I’m running it with Xming on Windows. Same thing shows up if I 
load a volume.


Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email: mark.wags...@einstein.yu.edu <mailto:mark.wags...@einstein.yu.edu>

einstein-logo-rgb

This email message and any accompanying attachments may contain 
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you are not the intended recipient(s), you are hereby notified that 
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*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 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
mailto:mark.wags...@einstein.yu.edu>> wrote:

Hi.

I’m a newbie to Freeview, hoping that this is a simple problem. 
When I open it (specifying the lh.pial surface), I get this view:



Anyone have an idea what’s going on here, is it an issue with the
screen resolution settings?

Thanks,

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email:mark.wags...@einstein.yu.edu
<mailto:mark.wags...@einstein.yu.edu>



This email message and any accompanying attachments may contain
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that the dissemination, distribution, and or copying of this
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at the email address above, delete this email from your computer,
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Re: [Freesurfer] Freeview not showing images

[Ruopeng Wang]

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 
> it (specifying the lh.pial surface), I get this view:
>  
> 
>  
> Anyone have an idea what’s going on here, is it an issue with the screen 
> resolution settings?
>  
> Thanks,
>  
> Mark
>  
> 
> Mark Wagshul, PhD
> Associate Professor
> Gruss Magnetic Resonance Research Center
> Albert Einstein College of Medicine
> Bronx, NY 10461
> 
> Ph: 718-430-4011
> FAX: 718-430-3399
> Email: mark.wags...@einstein.yu.edu 
>  
> 
> This email message and any accompanying attachments may contain privileged 
> information intended only for the named recipient(s). If you are not the 
> intended recipient(s), you are hereby notified that the dissemination, 
> distribution, and or copying of this message is strictly prohibited. If you 
> receive this message in error, or are not the named recipient(s), please 
> notify the sender at the email address above, delete this email from your 
> computer, and destroy any copies in any form immediately.
>  
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Re: [Freesurfer] questions about freeview quit unexpectly

[Ruopeng Wang]

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 wrong with this. DO 
you have any ideas about this? Thank you .

Best wishes
Shize




At 2018-06-27 00:54:45, "Dicamillo, Robert" 
 wrote:


Hello Shize,

Did you see the Finder bring up a window with a notification that
Freeview quit unexpectedly, with some choices to
click on for “ignore”, “report”, or “reopen” Freeview?    If so,
it could help if you select report, cut and paste (or take a
screenshot)
of the first page of the crash report and send it along.

- rob


On Jun 26, 2018, at 12:39 PM, 姜时泽 mailto:jiangshize1...@163.com>> wrote:

External Email - Use Caution


Dear fresurfer experts,
I am currently using freeview 2.0 to check some data. I am not
sure why it always quit unexpectedly when I try to load a volume.
my freeview is installed on OS 10.11.3 system. Would you please
help me to solve this problem. Thank you.
Best wishes
Shize




--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical
College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn 














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Re: [Freesurfer] fthresh function in tksurfer

[Ruopeng Wang]

Yes, I have put an option called z-order in the GUI to control order of 
rendering for overlays, labels and annoations. To use it you will need to 
download and install the nightly build from here:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview 
<https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview>

Best,
Ruopeng


> On Jun 9, 2018, at 11:04 AM, srishti goel <23srishtig...@gmail.com> wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Ruopeng,
> 
> I just wanted to check and see if there is any update about adding the option 
> of changing surface labels to come below overlays in Freeview.
> Thanks!
> 
> 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
> 
> 
> On Tue, May 29, 2018 at 2:40 PM, srishti goel <23srishtig...@gmail.com 
> <mailto:23srishtig...@gmail.com>> wrote:
> Thanks a lot Ruopeng, really appreciate it.
> 
> 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
> 
> 
> On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> It will be added very soon. I'll let you know when it is ready.
> 
> Best,
> Ruopeng
> 
> On 05/28/2018 05:35 PM, srishti goel wrote:
>> Hi Ruopeng,
>> 
>> Thank you so much! That option will be super helpful. Are you planning to 
>> add that option to Freeview soon?
>> 
>> 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
>> 
>> 
>> On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>> Hi Srishti,
>> 
>> In freeview surface labels are always displayed on top of overlays. I will 
>> add an option to change that.
>> 
>> Best,
>> Ruopeng
>> 
>> 
>>> On May 28, 2018, at 9:18 AM, srishti goel <23srishtig...@gmail.com 
>>> <mailto:23srishtig...@gmail.com>> wrote:
>>> 
>>> Hello,
>>> 
>>> I did use Freeview but I think using either TkSurfer or Freeview won't 
>>> matter because what I am trying to figure out is what the fthresh value 
>>> means for the map.
>>> From reading the archive, I understand that, for instance, fthresh value of 
>>> 0.3 will mean that the overlay displays 50% (1/10^3) threshold based on 
>>> intensity/ only voxels which are overlaid by 50% of the subjects. In my 
>>> case, the maps are visible at fthresh 0.1 and below but since these are 
>>> already thresholded maps from a meta-analysis I am not very clear on how to 
>>> interpret the fthresh here. Is it voxels overlaid by ~80% of studies?
>>> 
>>> The other thing I want to figure out is that right now when I view my 
>>> overlay with two other labels, the labels (when in solid color and not 
>>> outline) cover my overlay. But I would want it the other way round such 
>>> that the overlay comes on top of the solid colored labels. Does anyone know 
>>> how I can achieve that?
>>> 
>>> Thank you so much!
>>> 
>>> 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
>>> 
>>> 
>>> On Fri, May 25, 2018 at 10:09 AM, Douglas Greve >> <mailto:dgr...@mgh.harvard.edu>> wrote:
>>> I don't know anything about neuroelf, but unless your have a binarized map, 
>>> then the map is going to change when you change the threshold. BTW, if you 
>>> wan to use freeview, you can run tksurferfv with the same args as tksurfer
>>> 
>>> On 5/22/18 3:49 PM, srishti goel wrote:
>>>> 
>>>> 
>>>> Hello,
>>>> 
>>>> I am trying to vi

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

[Ruopeng Wang]

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 it 
be possible for you to reboot your machine (to flush opengl cache)? or 
even update your graphics driver?


Best,
Ruopeng


On 05/31/2018 02:06 PM, Rachel Smallwood Shoukry wrote:

Hello FreeSurfer developers,

I'm having an odd problem using freeview. When I open a set of volumes 
(wm and brainmask) and surfaces (both pial and white), everything 
seems to work fine. However, when I turn off the volumes to look at 
the 3D view and then turn them back on when switching back to 2D, the 
situation in Screenshot1 happens. The brainmask volume disappears in 
the coronal and axial planes but is still there in the sagittal. Also, 
it looks like a coordinate appears in large text written backwards 
superimposed over the surface outlines (mirrored, not just in reverse 
order), but it's not the coordinate from the current slice. For 
instance, this coronal slice says R 97.66 and the axial slice says R 
147.65. If I zoom in or out, the numbers get larger and smaller. The 
white matter volume is not affected. Everything works normally if I 
keep the volumes for viewing 3D rendering.


I have a similar thing happen when adding control points (it first 
happened when creating a new set, but if I load an existing set it 
happens also). The image is fine until I get to a specific coronal 
slice (usually just a few slices away from where I put the first 
control point), then the brainmask volume disappears in the coronal 
view but is still there in sagittal and axial. This time the displayed 
number is A 58.73 (mirrored), which is actually the label on the exact 
slice where brainmask disappears for this subject, but this number 
does change sometimes when scrolling through slices, but not on most 
slices and it doesn't change to match the current label.


If I close and re-open freeview with the same set of volumes and 
surfaces, they come up the way they should and remain as they should 
unless I turn off the volumes while looking at the 3D rendering or 
open the control point file again.


This has happened for multiple subjects/sets of files, and no messages 
appear in the terminal when this happens. I'm using a Linux with 
CentOS 6.9.


Any idea what could be causing this and/or how to fix it?

Thanks!
Rachel


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Re: [Freesurfer] fthresh function in tksurfer

[Ruopeng Wang]

It will be added very soon. I'll let you know when it is ready.

Best,
Ruopeng


On 05/28/2018 05:35 PM, srishti goel wrote:

Hi Ruopeng,

Thank you so much! That option will be super helpful. Are you planning 
to add that option to Freeview soon?


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


On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>> wrote:


Hi Srishti,

In freeview surface labels are always displayed on top of
overlays. I will add an option to change that.

Best,
Ruopeng



On May 28, 2018, at 9:18 AM, srishti goel
<23srishtig...@gmail.com <mailto:23srishtig...@gmail.com>> wrote:

Hello,

I did use Freeview but I think using either TkSurfer or Freeview
won't matter because what I am trying to figure out is what the
fthresh value means for the map.
From reading the archive, I understand that, for instance,
fthresh value of 0.3 will mean that the overlay displays 50%
(1/10^3) threshold based on intensity/ only voxels which are
overlaid by 50% of the subjects. In my case, the maps are visible
at fthresh 0.1 and below but since these are already thresholded
maps from a meta-analysis I am not very clear on how to interpret
the fthresh here. Is it voxels overlaid by ~80% of studies?

The other thing I want to figure out is that right now when I
view my overlay with two other labels, the labels (when in solid
color and not outline) cover my overlay. But I would want it the
other way round such that the overlay comes on top of the solid
colored labels. Does anyone know how I can achieve that?

Thank you so much!

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


On Fri, May 25, 2018 at 10:09 AM, Douglas Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

I don't know anything about neuroelf, but unless your have a
binarized map, then the map is going to change when you
change the threshold. BTW, if you wan to use freeview, you
can run tksurferfv with the same args as tksurfer


On 5/22/18 3:49 PM, srishti goel wrote:



Hello,

I am trying to view network based maps produced from a
meta-analysis using neuroelf on the surface in freesurfer.
The meta-analytic maps are thresholded maps that represent
the proportion of contrasts that activated at each voxel

I projected my maps on the surface using:
mri_vol2surf --src negative_allsocial_proportion.img
--regheader mni152_subject --hemi lh --o
./neg_allsocial_lh.nii --projfrac 0.5
Then to view it used:
tksurfer mni152_subject lh inflated -overlay
./neg_allsocial_lh.nii -fthresh 0.05
The issue I have is with the fthresh value. I read the wiki
and some stuff on archive about the fthresh value but I am
unsure what it exactly means and does. My issue is that the
display of my maps changes when I change the fthresh value
even though the maps have been k-thresholded using neuroelf
before exporting them to freesurfer. More area is marked up
when I decrease the threshold value from 0.1 to 0.05 and
nothing is visible above 0.1

Does anyone have any thoughts about what might be going on
there and how I can fix it?
Do I need to do something totally different from what I am
doing?

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



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Re: [Freesurfer] Freeview surface annotation outline line thickness

[Ruopeng Wang]

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 thicker?


With the default thickness, the outlines are difficult to make out in 
a multipanel figure. (The "edgethickness=" flag specifies the slice 
intersection crosshair with the surface, not the annotation outline 
thickness.)

Thanks,
-Kayle




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Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

[Ruopeng Wang]

BTW, that only applies to the dev version. 

Ruopeng

> On Apr 13, 2018, at 5:18 PM, Ruopeng Wang  wrote:
> 
> 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 that is what you 
>> mean)
>> 
>> cheers
>> Bruce
>> On Fri, 13 Apr 2018, Srinivasan, Dhivya wrote:
>> 
>>> Hi,
>>> 
>>> I am attempting  to view single anatomical ROI (say Right-Hippocampus) 
>>> overlaid on MRI image using freeview.How can I achieve this?
>>> 
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Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

[Ruopeng Wang]

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 that is what you 
> mean)
> 
> cheers
> Bruce
> On Fri, 13 Apr 2018, Srinivasan, Dhivya wrote:
> 
>> Hi,
>> 
>>  I am attempting  to view single anatomical ROI (say Right-Hippocampus) 
>> overlaid on MRI image using freeview.How can I achieve this?
>> 
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Re: [Freesurfer] Custom color map in Freeview

[Ruopeng Wang]

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.


Best,
Ruopeng

On 03/27/2018 03:59 PM, Anna Mynick wrote:

Hi all,

I’m wondering whether there’s a way to create a custom color map in 
Freeview that would operate as a alternative to the preset Greyscale, 
Heatmap, NIH, PET, Jet and GE Color options.


Ideally, I could assign each number value a given color, e.g. every 
“0” value in an .nii file is black, every “1” value is red, every “2” 
value is blue, every “3" is green and so on. I already have the RGB 
values worked out for each number value; I just need to know how to 
format this information and where to put it so that I can my custom 
colormap as an option in Freeview.


For my purposes, there would be no need to adjust the assigned colors 
based on the overall range of values. For instance, there would be no 
need to assign a different color value to a “1” value depending on 
whether the highest value in the overall .nii file is 1 or 100.


I did try reading the related conversation here 
 but 
I can’t seem to find the file it references, annotval2surfoverlay.m, 
in the Freesurfer directory.


Thanks very much for your help!
Anna



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Re: [Freesurfer] [Freesurfer/Freeview cutting]

[Ruopeng Wang]

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 yes, how? I cant 
> find a tutorial online for that. 
> tksurfer is not working, it crashes by it self. If i cant use freeview to 
> cut, do you suggest another alternative? 
> 
> thank you 
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Re: [Freesurfer] Fwd: Freeview update on Mac

[Ruopeng Wang]

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 
should be able to draw the ROI on both the surface and the volume.


Best,
Ruopeng


On 02/28/2018 02:07 PM, Sarah Cole wrote:

Great! Thank you so much, Andrew.

I downloaded the updated Freeview. I am still wondering how to draw an 
ROI on the surface in Freeview. I don't have the options.
Could you please let me know what command you are running to get the 
Freeview?


I am having the updated version Jan 2018.

Thanks,
Sarah

On Tue, Feb 27, 2018 at 11:40 AM, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:


Hi Sarah, I updated the wiki page. We actually just put up a
standalone, dev freeview app today.

best
Andrew


On February 27, 2018 at 11:38:57 AM, Sarah Cole
(coleashle...@gmail.com ) wrote:


Hi Doug/Zeke,

Could you please update the page for freeview update on Mac- if
it is available.

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview



Thanks,

S
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Re: [Freesurfer] viewing the flatten sheet

[Ruopeng Wang]

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 $h.flaten.patch.3d not in freeview 
nor in tksurfer it somehow collapse! my laptop is RAM:6G , core i5 , 
would you please help me how can I see the 2D flatten sheet ??


many thanks to any help you can provide me.

BRG,
Nazanin


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Re: [Freesurfer] Freeview

[Ruopeng Wang]

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 libpng12.so.0 but the apt-get install order nor 
> Synaptics could not find anything
>  
> Rekic
>  
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Re: [Freesurfer] Freeview

[Ruopeng Wang]

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 couldn’t find an appropriate answer in you 
> archives so I decided to write you.
> I could not find an 32 bit Version of Freeview in your archiv of previous 
> releases so I installed the latest version.
> Everytime I try to run it there is an Error appearing that says ‚cannot open 
> shared object file libpng12.so.0‘. Wanted to ask if you know if this Problem 
> has already been solved by another Freeview user.
> Or is there a 32 bit Version that I missed?
>  
> Thank you in advance
> Kindest regards
> Rekic Samir – Carinthian University of Applied Sciences, Austria
>  
>  
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Re: [Freesurfer] Reset view command in freeview

[Ruopeng Wang]

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 use 
-cam option. It allows you to rotate the view by 90 or 180 along a 
specific axis.


Best,
Ruopeng


On 12/11/2017 02:13 PM, Anna Mynick wrote:

Hi all,

I’m wondering whether there's a command-line equivalent to the the 
Reset View tool found in the Freeview GUI when you right-click a 
volume in 3d view. I tried using the -viewport tag (e.g. freeview -v 
myvolume.nii.gz -viewport coronal), but the problems with this are:


(1) Though the tag does change the viewpoint in which my volume is 
displayed, which /is /what I want, it also switches out of the 3d 
view, and my goal is to maintain the 3d view so I can view my region 
as an isosurface


(2) I’d like the option of choosing between anterior, posterior, 
superior, inferior, and left and right views, as in the Reset View 
tool menu, rather than just coronal, sagittal, and axial.


In other words, is there a way to open a volume to a specific view 
from the command line while maintaining 3d view?


Thanks for any help!

Best,
Anna


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

[Ruopeng Wang]

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 themselves they display correctly, however when I 
> display the orig volume and the volume versions of the ROIs- the label ROIs 
> suddenly change to be in the wrong plane. I have done this same thing before 
> and this hasn’t happened.
> Right now I am having to load just the orig and ROI labels then run the 
> command within freeview to load the label volumes to get it to display all 
> the images at the same time correctly.
> I would like to do it all in one command line at the same time.
>  
> Thanks,
>  
> Sara Sims 
> Graduate Research Fellow
> University of Alabama at Birmingham
> Department of Psychology
> 205-975-4060
> sno...@uab.edu 
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Re: [Freesurfer] Freeview display issue in Ubuntu 14/16 VM

[Ruopeng Wang]

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 host, and 
have noticed a problem in both Ubuntu 14 and 16 (but not 12) with 
Freeview. When a freeview window is opened, the black screen for 
displaying volumes/surfaces is necessarily at the front of the screen 
(i.e., nothing can be viewed in front of it). This makes viewing menu 
options and selecting volumes difficult and annoying, as well as 
working with other applications such as the terminal which cannot be 
placed over the freeview screen.


I’m wondering if others have experienced this or know of a solution?

Thanks,
Nick



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Re: [Freesurfer] Freeview Crashes!!

[Ruopeng Wang]

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 errors:
> 
> 1st Crash (While selecting color for the volume): 
> Volume - Colormap -Lookup Table option: 
> 
> 0�freeview.bin: symbol lookup error: freeview.bin: undefined symbol: 
> _ZN6QMutex12lockInternalEv
> 
> 
> 2nd Error/Crash: 
> Loaded lh.pial and rh.pial surfaces + a volume activated as an isosurface.
> Now while rotating the 3D window Freeview crashes with following error:
> 
> Did not find any volume info
> p9\d�Did not find any volume info
> p9\d�[0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>  
> 
>  ERROR: or try http://valgrind.org  on linux or man 
> libgmalloc on Apple to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
> run 
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named WS52 by wiki Thu Nov  9 
> 16:29:50 2017
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> 
> #
> 
> I don't think RAM/memory is an issue, as the computer has 65GB RAM. Any other 
> options/update I should try? I am planning to load multiple volumes as 
> isosurface in multiple colors, and show them with lh.pial and rh.pial. 
> 
> Thank you very much
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Re: [Freesurfer] Build Freeview on macOS

[Ruopeng Wang]

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 
> , 
> it mentions that "As of the writing of this document (June 2016) freeview is 
> unable to build on macOS 10.11 platforms and higher (El Capitan and higher)." 
> 
> Could we build Freeview on macOS now?
> 
> Best wishes,
> Aziz.
> 
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Re: [Freesurfer] Strange looking dtifit_FA.nii.gz in FreeView

[Ruopeng Wang]

It looks like just wrong window/level setting in freeview. Have you 
tried adjust it? You can do it semi-automatically by drawing a ROI with 
Ctrl + middle mouse button on the slice.


On 09/20/2017 12:12 PM, Linnea Marie Dramdal Borg wrote:


Hi,


My apologies, freeview_T207_dtifit_FA.nii.gz.png was not compressed 
properly. You will find it attached this time.


The issue appears to stem from FreeView, as the intensity in the FA 
picture is somehow reversed there, but not when opened in Fslview.


The representation in FreeView is fine, while the visualization goes 
wrong. FreeView also manages to do the path reconstructions in TRACULA 
even though the intensity appears inversed (see tractsOK.png). Why is 
this only happening to some of the files? The scanner settings were 
the same, and they are fine when opened in other viewer softwares.



Thank you,

Linnea Marie


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 


*Sent:* Tuesday, September 19, 2017 5:39:22 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* 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 Marie Dramdal Borg wrote:


Hi,


We have run TRACULA on a couple hundred subjects and the quality 
control shows that most of them are OK, but in a few subjects the 
dtifit_FA.nii.gz images look strange in FreeView. The image 
intensities appear reversed in FreeView (see 
freeview_T207_dtifit_FA.nii.gz.png) but look normal in Fslview (see 
Fslview_T207_dtifit_FA.nii.gz.png). T205 is an example of a subject 
that looks normal also in FreeView (see 
fslview-freeview_T205_dtifit_FA.nii.gz.png), as most of our 
subjects' dtifit_FA images do.



207's dwi_orig image looks fine in FreeView (see 
freeview_T207_dwi_orig.nii.gz.png) as do all its L1,L2,L3,V1,V2,V3 
etc. images.



I'm puzzled as to what has happened here. Since the image looks fine 
in Fslview I'm inclined to think this is a FreeView issue?




Thank you,


Linnea Marie





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Re: [Freesurfer] Freeview Strange Behavior

[Ruopeng Wang]

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 local 
images. For example, if I try to load images located in simba or mrs from nemo, 
I get something like the attached screenshot. If I copy the file locally, I 
don't see this behavior.

Marco also tried on his computer, replicating the same strange behavior. Any 
ideas on why this is happening?

Thank you very much!

Best,
--
Angel Torrado-Carvajal
Postdoctoral Research Fellow
Pain Neuroimaging Laboratory
MGH/HST Athinoula A. Martinos Center for Biomedical Imaging
Building 149, Room 1101, 13th Street, Charlestown, MA 02129 USA
atorradocarva...@mgh.harvard.edu | www.nmr.mgh.harvard.edu | @MGHMartinos


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

[Ruopeng Wang]

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 Marie Dramdal Borg wrote:


Hi,


We have run TRACULA on a couple hundred subjects and the quality 
control shows that most of them are OK, but in a few subjects the 
dtifit_FA.nii.gz images look strange in FreeView. The image 
intensities appear reversed in FreeView (see 
freeview_T207_dtifit_FA.nii.gz.png) but look normal in Fslview (see 
Fslview_T207_dtifit_FA.nii.gz.png). T205 is an example of a subject 
that looks normal also in FreeView (see 
fslview-freeview_T205_dtifit_FA.nii.gz.png), as most of our 
subjects' dtifit_FA images do.



207's dwi_orig image looks fine in FreeView (see 
freeview_T207_dwi_orig.nii.gz.png) as do all its L1,L2,L3,V1,V2,V3 
etc. images.



I'm puzzled as to what has happened here. Since the image looks fine 
in Fslview I'm inclined to think this is a FreeView issue?




Thank you,


Linnea Marie





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Re: [Freesurfer] Freeview in FreeSurfer 6.0

[Ruopeng Wang]

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)  
> wrote:
> 
> Dear FreeSurfer team,
> 
> I was viewing MNI152 template from FSL in freeview using FreeSurfer 6.0, and 
> somehow there was a shift between 1mm and 2mm template. The problem does not 
> show in FreeSurfer 5.3. Is there an error with freeview in FS6 or did the 
> command change?
> 
> The command I used is as follow:
> freeview $FSL_DIR/data/standard/MNI152_?mm_brain.nii.gz
> 
> Thank you!
> 
> Wu Jianxiao
> Department of Physiology & Department of Electrical and Computer Engineering
> National University of Singapore
> 
> 
> 
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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

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  wrote:
> 
> it seems that I should run it again
> thank you for your helps
> best regards
> 
> On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> OK. Actually I was wrong, the file has size of 0! I don’t know what happened 
> when you installed freesurfer or ran recon-all, but the file was not properly 
> written...
> 
>> On Aug 10, 2017, at 9:34 AM, Z Hessam > <mailto:z.hes...@gmail.com>> wrote:
>> 
>> I copy the *.tar.gz file, and open and install the program by terminal. I am 
>> confused because that work last week for this data, but now, this doesn't 
>> work.
>> for other datasets, i copy dicom files, then convert them with " recon-all 
>> -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 
>> fat_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 > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>> How did you put the data on your drive?
>> 
>>> On Aug 10, 2017, at 9:25 AM, Z Hessam >> <mailto: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 >> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>>> Wait, the file size looks too small. Only 1590 bytes. Did the data get 
>>> copied properly? Is your drive full? 
>>> 
>>>> On Aug 10, 2017, at 4:40 AM, Z Hessam >>> <mailto:z.hes...@gmail.com>> wrote:
>>>> 
>>>> it shows:
>>>> 
>>>> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 
>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>>> 
>>>> 
>>>> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang >>> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>>>> Hmm, if you run:
>>>> 
>>>> ls -l 
>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>>> 
>>>> what does it show?
>>>> 
>>>>> On Aug 9, 2017, at 4:47 PM, Z Hessam >>>> <mailto:z.hes...@gmail.com>> wrote:
>>>>> 
>>>>> of course:
>>>>> 
>>>>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
>>>>> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
>>>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
>>>>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
>>>>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>>>>> 
>>>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>>>  -1): read error
>>>>> MRIread failed: Unable to read from 
>>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>>>  -1): read error
>>>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>>>  -1): read error
>>>>> MRIread failed: Unable to read from 
>>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>>>  -1): read error
>>>>> 
>>>>> thanks a lot for your attention 
>>>>> 
>>>>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang >>>> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>>>>> Can you copy and paste the exact command line you ran and the error 
>>>>> message?
>>>>> 
>>>>> Ruopeng
>>>>> 
>>>>> 
>>>>> On 08/09/2017 02:21 PM, Z Hessam wrote:
>>>>>> 
>>>>>> I try it without \ chars, works for some other subjects
>>>>>> but it doesn't work for one of them,and now I can even open it with GUI, 
>>>>>> while I could open it before.
>>>>>> It seems that is time variant!
>>>>>> Should I run "recon-all ..." again for that subject?
>>>>>> 
>>>>>> 

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

[Ruopeng Wang]

OK. Actually I was wrong, the file has size of 0! I don’t know what happened 
when you installed freesurfer or ran recon-all, but the file was not properly 
written...

> On Aug 10, 2017, at 9:34 AM, Z Hessam  wrote:
> 
> I copy the *.tar.gz file, and open and install the program by terminal. I am 
> confused because that work last week for this data, but now, this doesn't 
> work.
> for other datasets, i copy dicom files, then convert them with " recon-all -i 
> STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 
> fat_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  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> How did you put the data on your drive?
> 
>> On Aug 10, 2017, at 9:25 AM, Z Hessam > <mailto: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 > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>> Wait, the file size looks too small. Only 1590 bytes. Did the data get 
>> copied properly? Is your drive full? 
>> 
>>> On Aug 10, 2017, at 4:40 AM, Z Hessam >> <mailto:z.hes...@gmail.com>> wrote:
>>> 
>>> it shows:
>>> 
>>> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>> 
>>> 
>>> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang >> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>>> Hmm, if you run:
>>> 
>>> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>> 
>>> what does it show?
>>> 
>>>> On Aug 9, 2017, at 4:47 PM, Z Hessam >>> <mailto:z.hes...@gmail.com>> wrote:
>>>> 
>>>> of course:
>>>> 
>>>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
>>>> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
>>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
>>>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
>>>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>>>> 
>>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>>  -1): read error
>>>> MRIread failed: Unable to read from 
>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>>  -1): read error
>>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>>  -1): read error
>>>> MRIread failed: Unable to read from 
>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>>  -1): read error
>>>> 
>>>> thanks a lot for your attention 
>>>> 
>>>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang >>> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>>>> Can you copy and paste the exact command line you ran and the error 
>>>> message?
>>>> 
>>>> Ruopeng
>>>> 
>>>> 
>>>> On 08/09/2017 02:21 PM, Z Hessam wrote:
>>>>> 
>>>>> I try it without \ chars, works for some other subjects
>>>>> but it doesn't work for one of them,and now I can even open it with GUI, 
>>>>> while I could open it before.
>>>>> It seems that is time variant!
>>>>> Should I run "recon-all ..." again for that subject?
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl >>>> <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>>>>> can you try it without all the \ characters?  You shouldn't need them if 
>>>>> it's all on one line
>>>>> 
>>>>> On Wed, 9 Aug 2017, Z Hessam wrote:
>>>>> 
>>>>> 
>>>>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \   
>>>>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
>>>>> mri_read(): couldn't determine type of file
>>>>> /media/hessam91/dri

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

[Ruopeng Wang]

How did you put the data on your drive?

> On Aug 10, 2017, at 9:25 AM, Z Hessam  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  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> Wait, the file size looks too small. Only 1590 bytes. Did the data get copied 
> properly? Is your drive full? 
> 
>> On Aug 10, 2017, at 4:40 AM, Z Hessam > <mailto:z.hes...@gmail.com>> wrote:
>> 
>> it shows:
>> 
>> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>> 
>> 
>> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>> Hmm, if you run:
>> 
>> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>> 
>> what does it show?
>> 
>>> On Aug 9, 2017, at 4:47 PM, Z Hessam >> <mailto:z.hes...@gmail.com>> wrote:
>>> 
>>> of course:
>>> 
>>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
>>> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
>>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
>>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>>> 
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>  -1): read error
>>> MRIread failed: Unable to read from 
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>  -1): read error
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>  -1): read error
>>> MRIread failed: Unable to read from 
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>  -1): read error
>>> 
>>> thanks a lot for your attention 
>>> 
>>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang >> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>>> Can you copy and paste the exact command line you ran and the error message?
>>> 
>>> Ruopeng
>>> 
>>> 
>>> On 08/09/2017 02:21 PM, Z Hessam wrote:
>>>> 
>>>> I try it without \ chars, works for some other subjects
>>>> but it doesn't work for one of them,and now I can even open it with GUI, 
>>>> while I could open it before.
>>>> It seems that is time variant!
>>>> Should I run "recon-all ..." again for that subject?
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl >>> <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>>>> can you try it without all the \ characters?  You shouldn't need them if 
>>>> it's all on one line
>>>> 
>>>> On Wed, 9 Aug 2017, Z Hessam wrote:
>>>> 
>>>> 
>>>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \   
>>>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
>>>> mri_read(): couldn't determine type of file
>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>>> MRIread failed: Unable to read from
>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>>> mri_read(): couldn't determine type of file
>>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>>> 
>>>> 
>>>> I use the example 4 in the "download and install" page of site
>>>> 
>>>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl >>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>>> wrote:
>>>> 
>>>>   hmmm, that looks ok, but it's hard to tell with all the
>>>>   backslashes and blank lines and such. Can you send the full
>>>>   command on a single line (e.g. by hitting up-arrow in the
>>>>   terminal window) and the actual output of freeview?
>>>> 
>>>>On Wed, 9 Aug 2017, Z Hessam wrote:
>>>> 
>>>> 
>>>> Hello Freesurfer Developers,
>>>> 
>>>> I have problem when I use "free