Re: [Freesurfer] longitudinal FreeSurfer help

[Swati Rane]

External Email - Use Caution

Hi Kersten,

Thanks for the reply. I think I am trying to understand the steps that follow.

Do I have to check whether my model with 2 random effects (intercept and time) 
is better than that with one (intercept)?

For the contrast I am interested in group wise longitudinal cortical thinning. 
And also, if the longitudinal thinning is different between groups.
Given that my X=[intercept time grp1 time*grp1 grp2 time*grp2 grp3 time*grp3 
age@timepoint1 gender]

How do I set up CM? Do I need to run the lme_mass_F multiple time per contrast 
I provide?
Will my CM be
For Longitudinal thinning in grp 1: [1 0 0 1 0 0 0 0 0 0]
For Longitudinal thinning in grp 2: [1 0 0 0 0 1 0 0 0 0]
For Longitudinal thinning in grp 3: [1 0 0 0 0 0 0 1 0 0]
For Longitudinal thinning difference grp 2 – grp 1: [1 0 0 -1 0 1 0 0 0 0]?

Can you explain the CM set-up described in the tutorial?

Thank you.

Swati
From:  on behalf of "Diers, Kersten 
/DZNE" 
Reply-To: Freesurfer support list 
Date: Thursday, March 12, 2020 at 5:19 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] longitudinal FreeSurfer help


External Email - Use Caution
Hello Swati,

your points 1-4 look fine, as far as I can see.

Regarding 5, the recommended spatiotemporal mass-univariate approach consists 
of calling three functions:


lme_mass_fit_EMinit, lme_mass_RgGrow, lme_mass_fit_Rgw


in that order. If that does not work, it is in my eyes possible to use the more 
simple mass-univariate approach using

lme_mass_fit_vw

as an alternative.

Regarding 6, which specific questions do you have?

Best regards,

Kersten


On Do, 2020-03-12 at 05:58 +, Swati Rane wrote:

External Email - Use Caution
Dear FreeSurfer experts,

I simply do not understand the LME setup for longitudinal analyses.

Here is what I have: 3 groups each with variable longitudinal data (in terms of 
umber of time points and interval between timepoints). I am interested in 
detecting if the rates of longitudinal atrophy in each of the 3 groups and 
whether it is significantly different between the 3 groups.


  1.  My Qdec file contains: fsid, fsid_base, time, age, group, gender
  2.  I read in the relevant files with (output of surf2surf, lh.cortex, 
lh.sphere)
  3.  I read the Qdec file removed the first column, obtained the subject IDs, 
keep numerical data and get a sorted ‘M’ matrix
  4.  X=[intercept time grp1 time*grp1 grp2 time*grp2 grp3 time*grp3 
age@timepoint1 gender]
  5.  After that, should I use voxel wise mass-univariate model or 
spatiotemporal mass-univariate model lme_mass_fit_vw or lme_mass_fit_EMinit?
  6.  After that I don’t understand the subsequent steps. Can you help me 
understand?

Any help is appreciated.

Thanks!
Swati

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[Freesurfer] Functional connectivity analysis ERROR: cannot find.../dof

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:
I cannot fix the problem that I mention in the subject. I put the output of the 
terminal below. I was doing functional connectivity analysis walkthrough 
tutorial and I followed until group analysis when applying "isxconcat-sess”. I 
cannot proceed because the “.dof” files are in "/sessx/rest/*” where x is a 
number from 0 to 9 and * indicates location. So I don’t know why this files are 
here and not in the analysis subdirectory i.e. “fc.lpccseed.lh”. 

What is the problem? How should I fix it?

Thank you for all the help!!

Sincerely,
Andrade. 

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Re: [Freesurfer] Group analysis

[Hengameh Marzbani]

External Email - Use Caution

thank you for your detailed and helpful explanation.

question 3: I mean just left and right. But what should I do if I want to
consider subcortical as well as left and right?

Best Regards
Hengameh

On Thu, Mar 12, 2020 at 12:07 AM Douglas N. Greve 
wrote:

>
>
> On 3/11/2020 4:21 PM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Thank you for the quick response.
>
> question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). I 
> can see the clusters by tksurfer. But, Can I have a text file included all 
> clusters?
>
> You can, the easiest way is to run mri_glmfit-sim and it will give you a
> list of clusters in a text file. If you set the cwp to 1, then it will give
> you all the clusters. See the help.
>
> question 3: I want to do the analyse by considering the whole brain. Is 
> correct to use --2spaces? and also I I want to visualize the results in both 
> hemisphere simultaneously. is it possible by freeview?
>
> Whole brain meaning left, right, and subcort or just left and right? If
> just left and right, then use --2spaces
>
> question 5: I can't understand what is the reason of using demean and 
> normalize. Would you mind explaining to me? And when is it necessary to use 
> them?
>
> Demeaning makes the design matrix better conditioned. But also if you are
> looking at the difference in average thickness between two groups
> regressing out, eg, age, then simply using age as a regressor will reduce
> the efficiency of the estimation because the age itself will have a
> non-zero mean, so the regression is left trying to figure out what part of
> the thickness average is due to the group and what part is due to age.
>
> Thank you so much.
>
> Hengameh
>
>
> On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve 
> wrote:
>
>>
>>
>> On 3/9/20 5:53 PM, Hengameh Marzbani wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hello Freesurfer developers,
>> > 1- I want to extract the uncorrected clusters from the uncorrected
>> significance maps obtained from mri_glmfit for structural data (to
>> illustrate cluster, size, location, and significance) like
>> abs.sig.cluster.summary (summary of clusters (text))which is obtained from
>> mri_glmfit-sim. Is there a way to do this?
>> Set the clusterwise p-value thresh to 1 (--cwp 1)
>> > 2- I don't see any clusters when I use cluster-based correction for
>> multiple comparisons (for example mri_glmfit-sim \  --glmdir lh.Area.glmdir
>> \ --sim mc-z 1 2 mc-z.abs\ --sim-sign abs --cache 4 neg \  --cwp
>> 0.05\  --2spaces). How much is it significant if I report the uncorrected
>> clusters?
>> Usually, reveiewers won't let you report exclusivly uncorrected results.
>> > 3- Are there new ways of looking at the whole brain together (not left
>> and right hemisphere separately)by Qdec and FSGD?
>> You can load both hemispheres into freeview, if that is what you mean
>> > 4- How can I do fdr correction in mri_glmfit-sim? what flag should I
>> use?
>> You can't, use mri_fdr. Run with --help to get docs
>> > 5- How can I demean and normalize the covariates when I use FSGD? what
>> flag should I use?
>> Add these lines in your FSGD file
>> DeMeanFlag 1
>> ReScaleFlag 1
>> >
>> > Thanks you in advance!
>> > Best regards,
>> > Hengameh
>> >
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
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>
>
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>
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[Freesurfer] freeview error

[Ortug, Alpen]

Hello FreeSurfer Experts,

I'm attempting to install Freesurfer. I am trying to test my installation.


$>recon-all -i sample-001.nii.gz -s bert -all




$>recon-all -s bert finished without error at


Wed Mar 11 19:09:43 EDT 2020
done

However, after this I am getting an error message when I try to open in 
Freeview. It is attached. I've searched the list and no similar errors have 
been reported.
Does anyone have any thoughts on how to trouble-shoot this one?

1) FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform:Ubuntu 
19.10 3) uname -a: Linux antalya 5.3.0-40-generic #32-Ubuntu SMP Fri Jan 31 
20:24:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 4) error file: see attached

Many thanks

Best



Alpen ORTUG, PhD
Post-doctoral Research Fellow

Division of Newborn Medicine

Boston Children's Hospital
Harvard Medical School
401 Park Dr.

Boston, MA 02215, USA




error .odt
Description: error .odt
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[Freesurfer] selxavg3-sess not working

[Nasiriavanaki, Zahra]

Hi Freesurferers

I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly, 
the  terminal output shows that it doesn't need updating for preprocessing and 
ends with this:  "Started at Thu Mar 12 10:48:09 EDT 2020
Ended   at Thu Mar 12 10:48:12 EDT 2020 preproc-sess done".  It seems that it 
just checks the preprocessing, but does not initiate the selxavg analysis. 
There is no error neither selxavg log file.

my command: selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh  -force

I appreciate any comments on this issue.

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


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Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

[Bruce Fischl]

Hi Frank

sorry, I've been busy with local deadlines that are over now. Can you send 
us the recon-all.log file? Or tar and gzip the entire subject dir and 
upload it to our ftp site? Apologies if any of this has been done.


cheers
Bruce


On Thu, 12 Mar 2020, Frank Chau wrote:


   External Email - Use Caution

Dear Douglas ,

How could I find out the root cause of this recon-all "exited with ERRORS"?
Does it mean there are flaws in the generated output? Or I could ignore this 
error warning? Thank you.

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas N. Greve 
Sent: 11 March 2020 21:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

it should not really affect it

On 3/10/2020 10:22 AM, Tim Schäfer wrote:

 External Email - Use Caution

Maybe Doug or Bruce should comment on that, but afaik that should not affect 
your analysis at all: recon-all will resample your data to 256x256x256 (as part 
of creating what FreeSurfer calls the 'conformed' version of the image) anyways.

The error you get, if I understand correctly from the logs, is that *after* the 
resampling, the FOV *still* is not 256.

Best,

Tim


On March 9, 2020 at 7:34 PM Frank Chau  wrote:


 External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Frank Chau 
Sent: 06 March 2020 22:17
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank



From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Tim Schäfer 
Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all.

Maybe somebody else has an idea...

Tim


On March 4, 2020 at 4:47 PM Frank Chau  wrote:


 External Email - Use Caution

Dear Tim,

I have checked the orig.mgz file and nothing usual was found (please see the 
attachment image)

For downloading my orig.mgz: 
https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0

Regards

Frank


From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Tim Schäfer 
Sent: 04 March 2020 23:27
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Dear Frank,

if you search the log in your Dropbox for 'error', this comes up:


ERROR! FOV=284.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.


Did you have a look at the orig.mgz?

Best,

Tim



On March 4, 2020 at 2:59 PM Frank Chau  wrote:


 External Email - Use Caution

Hello FreeSurfer Developers,

I ran a recon-all on a recent batch of T1 Nifti files and all ended with "exited with 
ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited with ERRORS at Sat Jan 11 
01:32:55 HKT 2020".

I've searched the email archive list and I found other researcher encountered same 
problem before. However, I am quite sure their root causes are not same as my case. 3 
possible causes were found in the email archive which about "exited with 
ERRORS":

   1.  The version of freesurfer (I have already used the latest 6.0.0 version)
   2.  Hard disk space (My computer have enough hard disk space)
   3.  sharing folder between virtual machine and original platform. (I use 
freesurfer in Mac OS which do not have this problem)

I uploaded the recon-all.log to my dropbox in case it's of any use.


1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c

2) Platform: MAC OS X 10.11.6

3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: 
Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64

4) recon-all.log, please download at:

https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0



Regards

Frank

---

FRANK  C Y CHAU



Research assistant

Division of Neurology

Department of Medicine



Tel: +852 6340 2553

Fax: 2872 5828



E-mail : cyfr...@hku.hk





Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 

Re: [Freesurfer] longitudinal FreeSurfer help

[Diers, Kersten /DZNE]

External Email - Use Caution

Hello Swati,

your points 1-4 look fine, as far as I can see.

Regarding 5, the recommended spatiotemporal mass-univariate approach consists 
of calling three functions:


lme_mass_fit_EMinit, lme_mass_RgGrow, lme_mass_fit_Rgw


in that order. If that does not work, it is in my eyes possible to use the more 
simple mass-univariate approach using

lme_mass_fit_vw

as an alternative.

Regarding 6, which specific questions do you have?

Best regards,

Kersten


On Do, 2020-03-12 at 05:58 +, Swati Rane wrote:

External Email - Use Caution
Dear FreeSurfer experts,

I simply do not understand the LME setup for longitudinal analyses.

Here is what I have: 3 groups each with variable longitudinal data (in terms of 
umber of time points and interval between timepoints). I am interested in 
detecting if the rates of longitudinal atrophy in each of the 3 groups and 
whether it is significantly different between the 3 groups.


  1.  My Qdec file contains: fsid, fsid_base, time, age, group, gender
  2.  I read in the relevant files with (output of surf2surf, lh.cortex, 
lh.sphere)
  3.  I read the Qdec file removed the first column, obtained the subject IDs, 
keep numerical data and get a sorted ‘M’ matrix
  4.  X=[intercept time grp1 time*grp1 grp2 time*grp2 grp3 time*grp3 
age@timepoint1 gender]
  5.  After that, should I use voxel wise mass-univariate model or 
spatiotemporal mass-univariate model lme_mass_fit_vw or lme_mass_fit_EMinit?
  6.  After that I don’t understand the subsequent steps. Can you help me 
understand?

Any help is appreciated.

Thanks!
Swati

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[Freesurfer] mri_glmfit and mri_glmfit-sim

[Varun Chandran]

External Email - Use Caution

Dear FS experts,

I am looking at the relationship between the cortical thickness and a
behaviour measure, while controlling for the effects of age and gender. In
this analysis, I am using CT_AT.fsgd, contrast_pos.txt and a
contrast_neg.txt.

GroupDescriptorFile 1
Title Autistictraits
Class AT
Variables Age Gender   AT

Input   Con_P001   AT   -4.142-0.42821
Input   Con_P002   AT   -8.142-0.42831

My separate two contrast files:

Contrast_pos.txt  0  0   0 1

Contrast_neg.txt  0  0   0 -1

mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C
Contrast91_pos.txt --surf fsaverage lh --cortex --glmdir
glmdirlhposlat.glmdir

mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C
Contrast91_neg.txt --surf fsaverage lh --cortex --glmdir
glmdirlhneglat.glmdir

mri_glmfit-sim --glmdir glmdirlhposlat.glmdir --cache 1.3 pos --cwp 0.05

mri_glmfit-sim --glmdir glmdirlhneglat.glmdir --cache 1.3 neg --cwp 0.05

By changing the commands appropriately, I am looking at the right
hemisphere too.

Can anyone please help me to clarify, if I am applying the command lines
correctly? Any sort of help would be very much appreciated. Thanks !

best,
Varun Arunachalam Chandran
PhD scholar (Neurosciences)

*School of Psychology and Clinical Language Sciences, University of
Reading, Harry Pitt Building, *
*Whiteknights campus, Reading-RG6 7BE,*
*Berkshire, United Kingdom.*
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Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

[Frank Chau]

External Email - Use Caution

Dear Douglas ,

How could I find out the root cause of this recon-all "exited with ERRORS"? 
Does it mean there are flaws in the generated output? Or I could ignore this 
error warning? Thank you.

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: 11 March 2020 21:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

it should not really affect it

On 3/10/2020 10:22 AM, Tim Schäfer wrote:
>  External Email - Use Caution
>
> Maybe Doug or Bruce should comment on that, but afaik that should not affect 
> your analysis at all: recon-all will resample your data to 256x256x256 (as 
> part of creating what FreeSurfer calls the 'conformed' version of the image) 
> anyways.
>
> The error you get, if I understand correctly from the logs, is that *after* 
> the resampling, the FOV *still* is not 256.
>
> Best,
>
> Tim
>
>> On March 9, 2020 at 7:34 PM Frank Chau  wrote:
>>
>>
>>  External Email - Use Caution
>>
>> Dear Tim,
>>
>> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
>> affect the process Recon-all? If yes, how would it impact my output results?
>>
>> Regards
>>
>> Frank
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Frank Chau 
>> 
>> Sent: 06 March 2020 22:17
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>
>>  External Email - Use Caution
>>
>> Dear Tim,
>>
>> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
>> affect the process Recon-all? If yes, how would it impact my output results?
>>
>> Regards
>>
>> Frank
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Tim Schäfer 
>> 
>> Sent: 05 March 2020 2:25
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>
>>  External Email - Use Caution
>>
>> Thanks for providing the image. Looks fine to me as well.
>>
>> What is a bit strange is that when running `mri_info` on the file you 
>> provided, it shows a FOV of 256 (not 284!) for me, so I have no idea why 
>> this error is triggered in recon-all.
>>
>> Maybe somebody else has an idea...
>>
>> Tim
>>
>>> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>>>
>>>
>>>  External Email - Use Caution
>>>
>>> Dear Tim,
>>>
>>> I have checked the orig.mgz file and nothing usual was found (please see 
>>> the attachment image)
>>>
>>> For downloading my orig.mgz: 
>>> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>>>
>>> Regards
>>>
>>> Frank
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Tim Schäfer 
>>> 
>>> Sent: 04 March 2020 23:27
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>>
>>>  External Email - Use Caution
>>>
>>> Dear Frank,
>>>
>>> if you search the log in your Dropbox for 'error', this comes up:
>>>
>>> 
>>> ERROR! FOV=284.000 > 256
>>> Include the flag -cw256 with recon-all!
>>> Inspect orig.mgz to ensure the head is fully visible.
>>> 
>>>
>>> Did you have a look at the orig.mgz?
>>>
>>> Best,
>>>
>>> Tim
>>>
>>>
 On March 4, 2020 at 2:59 PM Frank Chau  wrote:


  External Email - Use Caution

 Hello FreeSurfer Developers,

 I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
 "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 
 exited with ERRORS at Sat Jan 11 01:32:55 HKT 2020".

 I've searched the email archive list and I found other researcher 
 encountered same problem before. However, I am quite sure their root 
 causes are not same as my case. 3 possible causes were found in the email 
 archive which about "exited with ERRORS":

1.  The version of freesurfer (I have already used the latest 6.0.0 
 version)
2.  Hard disk space (My computer have enough hard disk space)
3.  sharing folder between virtual machine and original platform. (I 
 use freesurfer in Mac OS which do not have this problem)

 I uploaded the recon-all.log to my dropbox in case it's of any use.


 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c

 2) Platform: MAC OS X 10.11.6

 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
 x86_64

 4) recon-all.log, please download at:

 https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0



 Regards

 Frank

 

Re: [Freesurfer] Freeview error: GLXBadContext

[fsbuild]

External Email - Use Caution

Hello Alek,
When you say you are running Ubuntu 14 via a Windows 10 PC, do you mean you are 
running the add-on windows subsystem for linux (known as WSL) that allows you 
run an Ubuntu shell on Windows 10?  And then when you say you are 
remotely viewing things, does that mean you are remotely logging into that 
Windows machine?
If you are in fact using WSL, then for X Window based GUI application like 
Freeview to run in WSL, you need to have an X server installed and running on 
the windows side, e.g., Xming. Then WSL can send X windows based graphics 
from the Linux shell back to Xming on the Windows side for rendering.. 
But Windows OS has to be able to handle rendering the graphics thru 
Xming using the drivers for whatever the graphics card/hardware is (which could 
include a GPU).
If you look at this thread for the same error you posted, but on a pure linux 
desktop,https://stackoverflow.com/questions/9769613/x-error-badalloc-glx-badcontext-on-intelsandybridge-intel-hd-graphics-3000,
 it reads to me like this may have been solved by updating the *mesa* libraries 
in linux which support displaying graphics (directly on the linux OS driving 
the graphics card). Translating this to the Windows WSL environment 
however - it would seem the same error could be from the graphics received by 
the X-server on the Windows side not being compatible/supported by the graphics 
drivers/hardware there. It might also have something to do with how the 
X-server is configured.
I don’t have much experience with WSL, but I would think that in the Ubuntu 
linux shell you’d want to set display for the console,
$ export DISPLAY=:0
Then it sounds like that /usr/bin/xeyes or other *simple* X programs already 
get displayed correctly,
$ /usr/bin/xeyes
Do you get the same error if you run a simple freeview command to open a single 
volume, e..g.
$ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz
I would trytheabove directly on the windows machine (not remotely 
logged in).
- R.
On Mar 11, 2020, at 10:46, Duvnjak, Aleksandar 
aleksandar.duvnja...@imperial.ac.uk 
wrote:External Email - Use 
CautionDear FreeSurfer 
experts,Version: Freesurfer version 6.0Platform: Ubuntu 14.04 (Via a Windows 10 
PC)Upon completion of our first FreeSurfer job, in which we ran an array 
on ~50 subjects, we have tried to view the basic outputs (e.g. T1.mgz) using 
both freeview -v and FSLview. Upon running freeview -v, the app opens but shows 
nodiscernibleimage (see screengrab below). Upon exiting the viewing 
platform the command line reads:X Error: GLXBadContext 150 
Extension:  143 (Uknown extension) Minor opcode: 5 (Unknown 
request) Resource id: 0x8000c8I have found reference to this error 
in the archives 
at:https://www.mail-archive..com/freesurfer@nmr.mgh.harvard.edu/msg30865.htmland
 much like with this original query, we are running freeview remotely via a 
high-performace-computing system, and when we type glxgears at the command line 
spinning gears do popup.Furthermore, (and although this does not relate 
directly to Freesurfer, it may provide additional useful information) upon 
trying to view the same T1.mgz file with FSLview rather than freeview we 
receive the message "missing header/image file" within the viewer but no error 
in the command line.We appreciate this may be a simple solution, however 
as it is our first time running FreeSurfer, it is difficult to know how to 
proceed. I have attached the recon-all report log for the subject attempting to 
be viewed in the screengrab below.pastedImagebase640.pngKind 
regards,Aleks 
Duvnjakrecon-all.log___Freesurfer
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