Re: [Freesurfer] freeview errors

[Ruopeng Wang]

Can you try just loading one surface? Such as:

freeview -f /media/seagate_external/subject/surf/lh.inflated

Does it load? What if:

mris_info /media/seagate_external/subject/surf/lh.inflated

or even just:

ls -l /media/seagate_external/subject/surf/lh.inflated

Does it show any error?

On 01/07/2015 12:13 PM, Hirsch, Gabriella wrote:

Hello,

I sent in a message yesterday but to no avail. I thought I would add a 
little more info about the error message I'm receiving. I am trying to 
view surfaces in 3D using Freeview on my own subject data via this 
script from the Freesurfer website (replacing the subject name);


freeview -f 
good_output/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 
\

good_output/surf/lh.inflated:visible=0 \
good_output/surf/lh.white:visible=0 \
good_output/surf/lh.pial

While Freeview loads correctly, I get an error message in the terminal 
AND the GUI upon loading:


MRISread(/surf/lh.pial): could not open file
MRISread(/media/seagate_external/subject/surf/lh.inflated): could not 
open file
MRISread(/media/seagate_external/subject/surf/lh.inflated): could not 
open file
MRISread(/media/seagate_external/subject/surf/lh.white): could not 
open file
MRISread(/media/seagate_external/subject/surf/lh.pial): could not open 
file


I've checked all the files and each one exists in the correct path. 
I've tried loading the subject data from both a drobo and from an 
external hardrive with no luck - same errors.  I've also gone through 
the website/google but I can't seem to find a fix for this.


Any ideas on what's going on? Apologies for the repeat.

Thanks!
Gabriella


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Re: [Freesurfer] Freeview question: using "line profile"

[Ruopeng Wang]

I think you need to create 2 sets of way points as iso-lines. You can do 
that from File -> New Point Set and select 'way point'. Then you should 
be able to use the line profile tool.


On 01/14/2015 04:55 PM, Albrecht, Daniel S. wrote:

Hello,

I'm having trouble using the "line profile" tool in FreeView. I have a 
PET image overlaid on an MR image, and would like to view a line 
profile of a rectangular ROI on the PET image. I assumed that the 
"line profile" selection in "Tools" would be able to do this, but I 
haven't been able to get it to work and haven't been able to find any 
documentation on using the tool. Can anyone provide any information on 
this? Thanks,


Dan


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Re: [Freesurfer] GLM analysis freeview error

[Ruopeng Wang]

That option is only available in the development version of freeview. 
You can try removing ":annot_ouline=1" from the command-line and turn it 
on manually from the GUI.


Best,
Ruopeng

On 01/15/2015 01:28 PM, Hirsch, Gabriella wrote:

Hello,

I have encountered a silly error message I'm hoping someone can help 
me with. I've been following the GLM analysis tutorial 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) 
and have managed to go through all the steps; however I am now having 
issues visualizing my results.


Having called the command:

freeview -f $SUBJECTS_DIR/fsaverage/surf/ 
lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.control_CVI.glmdir/contrast/sig.mgh:overlay_threshold=4,5 
-viewport 3d


I get the error:

Unrecognized sub-option flag 'annot_outline'.

Any ideas on what this might be?

I appreciate your help.

Thanks!
Gabriella


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Re: [Freesurfer] Custom color lookup table

[Ruopeng Wang]

I can confirm this bug on Mac (It does not happen on Linux). I'll look 
into it.


Best,
Ruopeng

On 01/21/2015 03:11 PM, Mateus Aranha wrote:

Hi all,

I recently installed freesurfer on my mac, and I'm having a small 
problem with freeview. If I load a segmentation file, and then try to 
associate it with a custom color lookup table, freeview stops 
responding. Even if I was to use an exact copy of 
/Applications/freesurfer/FreeSurferColorLUT.txt, the problem still 
persists:


cp -i /Applications/freesurfer/FreeSurferColorLUT.txt \ 
~/Documents/CustomColor.txt


I will try to re-install the program, but I first wanted to check if 
anyone has ever encountered issues with custom color tables.


See info below:


MacBook Air (13")
OS X Yosemite (Version 10.10)
Processor: 1,4 GHz Intel Core i5; x86_64)
Memory: 4GB 1600 MHz DDR3


I first downloaded XQuartz 2.7.6 and then downloaded/installed latest 
versions of freesurfer and freeview:


http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview

I'd really appreciate your feedback. Thank you very much!


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Re: [Freesurfer] Problems with quantitative T1 images and Freeview

[Ruopeng Wang]

Would it be possible to send us an image file that you had problem with?

Best,
Ruopeng

On Feb 2, 2015, at 7:38 AM, Pernille Iversen  wrote:

> Dear Freesurfer team,
> We calculate our T1 images from quantitative sequences. I have tried to 
> process one of these images with the FS pipeline and it finishes apparently 
> without errors. However, when I try to load any of the .mgz files in 
> Freeview, the images appears as a white box. Changing the slider settings for 
> opacity, window, level, min or max does not help. The only way I can get a 
> hint of a brain (including a lot of noise) is to change color map to 
> colorlut, so maybe Freeview has problems with showing these images.
> 
> Any suggestions how to proceed? Are there any special settings I need for the 
> image generation?
> 
> Thanks in advance.
> 
> Pernille
> 
> 
> 
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Re: [Freesurfer] Freeview colorbar with command line & white background?

[Ruopeng Wang]

Hi Xiuming,

You can’t change color scale or change the background color from the 
command-line. You can change the background color from the GUI: Edit -> 
Preferences. I will add these options in the command-line.

Best,
Ruopeng

On Feb 6, 2015, at 11:52 AM, Xiuming Zhang  wrote:

> Dear freesurfer experts,
> 
> I have two quick questions regarding freeview.
> 
> (1) The color bar is still from 0 to 1 even if I am overlying a super 
> small-valued (1e-6) map on lh.inflated. Here is what I did:
> 
> freeview -f lh.inflated:overlay=lh.map:overlay_method=linear:edgethickness=0 
> -viewport 3d -colorscale
> 
> In GUI, I can right click the colorbar and choose "Show colorer -> 
> lh.inflated". Is it possible to do it in command line?
> 
> (2) Is it possible to set the background to be white instead of black? It 
> would be great if it can also be automated (i.e., with command line). Here is 
> what I have so far.
> 
> freeview -f rh.inflated:overlay=rh.map -ss ./rh
> 
> Thank you very much in advance for your help!
> 
> Best regards,
> Xiuming
> 
> ᐧ
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Re: [Freesurfer] Freeview colorbar with command line & white background?

[Ruopeng Wang]

Hi Xiuming,

I think the color scale always display the full scale which includes the 
inverted part. I understand it is not ideal in this case. I will improve it.

Best,
Ruopeng

On Feb 6, 2015, at 8:26 PM, Xiuming Zhang (Ming)  
wrote:

> Hi Ruopeng,
> 
> Thanks a lot for helping clarify this!
> 
> May I ask a follow-up question? Why am I getting a symmetric-around-0 
> colorbar (please see the attachment)? I only have values from 3.99e-6 to 
> 1.2e-5.
> 
> 
> 
> Thank you very much!
> 
> Best regards,
> Xiuming (Ming)

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Re: [Freesurfer] problem loading LUT in freeview on Mac

[Ruopeng Wang]

Hi Ronald,

No the issue is still there. I will let you as soon as it is fixed. The 
default LUT is FreeSurferColorLUT.txt. But it is hard-coded into the binary.

Best,
Ruopeng

On 02/10/2015 12:03 PM, Ronald Pierson wrote:
> When loading a lookup table in freeview on the Mac with version 5.3 the 
> program freezes.  I saw a similar issue was reported previously.  Is there an 
> fix or patch for this?  I tried modifying the FreeSurferColorLUT.txt, but 
> that doesn’t change the default colors.  If there is no patch for this, is 
> there a different way to work around it?  What LUT is it loading as default?  
> Or is it hard coded into freeview?
>
> Thanks,
>
> Ronald Pierson
>
>
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Re: [Freesurfer] problem loading LUT in freeview on Mac

[Ruopeng Wang]

Hi Ronald,

This issue has been fixed. If you want to download the latest Freeview 
build, please follow the instructions on the following page:

http://surfer.nmr.mgh.harvard.edu/fswiki/Download

Best,
Ruopeng

On 02/10/2015 12:03 PM, Ronald Pierson wrote:
> When loading a lookup table in freeview on the Mac with version 5.3 the 
> program freezes.  I saw a similar issue was reported previously.  Is there an 
> fix or patch for this?  I tried modifying the FreeSurferColorLUT.txt, but 
> that doesn’t change the default colors.  If there is no patch for this, is 
> there a different way to work around it?  What LUT is it loading as default?  
> Or is it hard coded into freeview?
>
> Thanks,
>
> Ronald Pierson
>
>
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Re: [Freesurfer] freeview registration

[Ruopeng Wang]

Yes, I think I fixed it.

On Mar 2, 2015, at 11:21 AM, Douglas N Greve  wrote:

> 
> I know that Ruopeng was fixing it a few months ago. Ruopeng, did you finish 
> that fix?
> doug
> 
> On 03/02/2015 10:28 AM, Xiaomin Yue wrote:
>> Hi Doug,
>> 
>> thanks for your response.  You are right that the freeview in v5.3 doesn't 
>> generate the registration file correctly. However, the newest development 
>> version of freeview can generate a lta registration file correctly with 
>> correct source and target volume.  then, a registration file in reg format 
>> can be generated using lta_convert included in the development version of 
>> freesurfer.  It is much easier and precise to manually adjust the 
>> registration using freeview than tkregister.   It might be useful to include 
>> a tool using freeview to manually adjust registration in the next freesurfer 
>> release.
>> 
>> Xiaomin
>> 
>> 
>> Date: Sun, 1 Mar 2015 13:57:52 -0500
>> From: gr...@nmr.mgh.harvard.edu
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] freeview registration
>> 
>> 
>> I think that freeview does not correctly generate the registration file. You 
>> can use it to check the regsitration, but us tkregister if  you need to edit 
>>  it.
>> doug
>> 
>> 
>> On 2/27/15 10:18 AM, Xiaomin Yue wrote:
>> 
>>Hi All,
>> 
>>After using freeview to manually adjust the registration between a
>>functional and T1.mgz generated by bbregister, I saved the
>>registration file in freeview as lta format, which seems the only
>>option.  However, the registration file has same file name for
>>source and target volume.  So, when loading it again to freeview,
>>the registration is totally wrong.   In order to avoid the
>>problem, I converted the register.dof6.dat to lta formation, where
>>the lta file has correct source and target volume name.  Then, I
>>loaded the lta file generated from register.dof6.dat, did manual
>>adjustment, and then saved adjusted registration as a lta file.
>> the final lta file has same problem.   I am using freesurfer 5.3.
>> Any suggestion is appreciated.
>> 
>>Thanks,
>>Xiaomin
>> 
>> 
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>> 
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> -- 
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] encounter a problem when using freesurfer

[Ruopeng Wang]

Hi,

You can run the following command in a console to reset freeview settings:

rm ~/.config/Massachusetts\ General\ Hospital/freeview.conf 

Then run freeview again.

Best
Ruopeng

On Mar 22, 2015, at 12:12 AM, zhaoshanshan  wrote:

> 
> dear,
> I have some problems when using Freeview, and find no solution on 
> Freesurfer wiki.
> The problem is that I miss the toolbar at the top of the Display window 
> of Freeview. Below is the screenshot of my Freeview window.
> 
> — 
> But the initial window is like :
> 
> 
> Now it’s very inconvenient to change different 
> views(sagittal,coronal,axial,3d) and change the layout of the image. To do 
> this ,I have to open the menu to select different views.
> I want to know if there is any way to recover the toolbar at the top?
> Appreciate for your answer.Thanks!
> 
> Grace
> Sent with Airmail
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Re: [Freesurfer] Fwd: Questions on labeling ROIs with values on inflated cortical surfaces

[Ruopeng Wang]

Hi Xixi,

Do you want to create a customized annotation file to load on a surface? 
or do you want to load multiple labels with different colors?


Best,
Ruopeng

On 06/16/2015 03:33 PM, Xixi Wang wrote:

Hi FreeSurfer users,

I’m trying to label different ROIs with corresponding decoding 
accuracies on inflated cortical surfaces. I’d like to create something 
like Figure 4B on 
http://freesurfer.net/fswiki/FreeSurferAnalysisPipelineOverview. 
Instead of using the default colormap, I’d like to generate my own 
colormap (i.e. grayscale or jet colormap) so that for each region, 
different color stands for different decoding accuracy value. I'm not 
sure whether I could do this in FreeSurfer, any advice would be 
greatly appreciated!


Best,
Xixi



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Re: [Freesurfer] [FreeSurfer] Axis of Alignment

[Ruopeng Wang]

Hi Joseph,

In freeview you can use "Tools"->"Transform Volume" to reorient volumes.

Best,
Ruopeng

On 08/11/2015 02:59 PM, Bruce Fischl wrote:
> Ruopeng should be able to help you out
>
> cheers
> Bruce
> On Tue, 11 Aug 2015, fmri wrote:
>
>> Is there a wiki instruction block on how to reorient all volumes?
>>
>> Thanks
>>
>> On Aug 11, 2015, at 6:13 AM, Bruce Fischl wrote:
>>
>>> Hi Joseph,
>>>
>>> no it shouldn't matter to us what the angle is as long as it's in
>>> approximately the right orientation. You could reorient the volumes in
>>> freeview if you wanted, but I don't think it's necessary
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 10 Aug 2015, fmri wrote:
>>>
 Hello FreeSurfer experts,

 When MRI slices are not aligned to a more perfect plane of axis as shown 
 in the 3D render attached. The sagittal slice is Not in-line with the 
 midsagittal plane of the cerebral cortex.

 All orthogonal slices are viewed in some Uneven angle, this is 
 demonstrated in the Coronal image attached.

 The coronal slice demonstrates the left hemisphere of the brain in view 
 Before the right hemisphere.

 This has become trouble some for editing and review purposes.

 The greater concern is that we believe this could be affecting 
 FreeSurfers' ability to distinguish critical areas in the temporal lobes.

 Does the incorrect alignment of slices -to- brain anatomy matter when 
 generating segmentations and parcellations?

 If so is there a way to correct these angels before the recons begins to 
 get better results in labeling segmentations and parcellations?

 Or is there a way to correct these angles for viewing and editing purposes?

 Any thoughts on the matter are appreciated,

 Thanks so much,

 Joseph

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Re: [Freesurfer] pial-outer-smoothed misalignment

[Ruopeng Wang]

Would it be possible to send me the surface and the volume that do not 
align in freeview?


Thanks,
Ruopeng

On 08/13/2015 11:46 AM, Roan LaPlante wrote:

Hello,

I am trying to use mris_compute_lgi to create the smoothed pial 
surface with no gyri, and then use this surface for a different 
purpose than the LGI.


To do this I simply modified a version of the mris_compute_lgi script 
to run up until the creation of the *h.pial-outer-smoothed surfaces.


When examining the surface in tkmedit it appears to align with the 
pial surface correctly. But I tried to open the surfaces in freeview 
and saw that the surface coordinates do not match the volume. At a 
glance the misalignment may only be a translation in the A/P direction.


Is there a reason why the coordinates in this surface differ from the 
subject RAS space and what transformation is tkmedit applying to align 
them?


thanks,

--
Roan LaPlante
Athinoula A. Martinos Center for Biomedical Imaging



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Re: [Freesurfer] Error when loading ?h.aparc.annot on fsaverage_sym ?h.pial

[Ruopeng Wang]

Would it be possible to send us lh.pial and lh.aparc.annot that caused the 
crash?

Best,
Ruopeng

On Aug 28, 2015, at 10:59 AM, Matthieu Vanhoutte  
wrote:

> I launched freeview, then added manually lh.pial and rh.pial of 
> fsaverage_sym. A this point all is OK.
> 
> Then it crashed when I try to load graphically lh.aparc.annot or 
> rh.aparc.annot. I viewed that in freesurfer mailing, this problem has been 
> told in the beginning of 2014 but nothing afterthen.
> 
> Do you have a comman line way to manage to load annotation file under 
> freeview ?
> 
> Matthieu
> 
> 2015-08-28 16:42 GMT+02:00 Douglas Greve :
> what is your command line? Can you run it without the annotation?
> 
> 
> On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote:
>> Dear Freesurfer experts,
>> 
>> It seems impossible to load ?h.aparc.annot annotation file on ?h.pial 
>> surface of the fsaverage_sym subject. When I try under freeview, it crashes 
>> and gives me this error :
>> 
>> Did not find any volume geometry information in the surface
>> pB Did not find any volume geometry information in the surface
>> pB reading colortable from annotation file...
>> colortable with 1036 entries read (originally 
>> /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)
>> [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 yakuza by matthieu Fri Aug 
>> 28 11:32:19 2015
>> [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
>> 
>> Could you help me please ?
>> 
>> Best regards,
>> 
>> Matthieu
>> 
>> 
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Re: [Freesurfer] Error when loading ?h.aparc.annot on fsaverage_sym ?h.pial

[Ruopeng Wang]

If the files are not big, you can just email them to me. Otherwise you can use 
file drop:

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Ruopeng

On Aug 28, 2015, at 11:23 AM, Matthieu Vanhoutte  
wrote:

> I can do it. Where could I send you these files ?
> 
> Best regards,
> 
> Matthieu
> 
> 2015-08-28 17:12 GMT+02:00 Ruopeng Wang :
> Would it be possible to send us lh.pial and lh.aparc.annot that caused the 
> crash?
> 
> Best,
> Ruopeng
> 
> On Aug 28, 2015, at 10:59 AM, Matthieu Vanhoutte 
>  wrote:
> 
>> I launched freeview, then added manually lh.pial and rh.pial of 
>> fsaverage_sym. A this point all is OK.
>> 
>> Then it crashed when I try to load graphically lh.aparc.annot or 
>> rh.aparc.annot. I viewed that in freesurfer mailing, this problem has been 
>> told in the beginning of 2014 but nothing afterthen.
>> 
>> Do you have a comman line way to manage to load annotation file under 
>> freeview ?
>> 
>> Matthieu
>> 
>> 2015-08-28 16:42 GMT+02:00 Douglas Greve :
>> what is your command line? Can you run it without the annotation?
>> 
>> 
>> On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote:
>>> Dear Freesurfer experts,
>>> 
>>> It seems impossible to load ?h.aparc.annot annotation file on ?h.pial 
>>> surface of the fsaverage_sym subject. When I try under freeview, it crashes 
>>> and gives me this error :
>>> 
>>> Did not find any volume geometry information in the surface
>>> pB Did not find any volume geometry information in the surface
>>> pB reading colortable from annotation file...
>>> colortable with 1036 entries read (originally 
>>> /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)
>>> [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 yakuza by matthieu Fri 
>>> Aug 28 11:32:19 2015
>>> [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
>>> 
>>> Could you help me please ?
>>> 
>>> Best regards,
>>> 
>>> Matthieu
>>> 
>>> 
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
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>> Freesurfer mailing list
>>

Re: [Freesurfer] Error when loading ?h.aparc.annot on fsaverage_sym ?h.pial

[Ruopeng Wang]

Thanks for sending me the files. I have no issue loading the annotation file 
using the latest freeview build. I assume you are still running an old version 
that comes with freesurfer 5.3 official release. You can download the latest 
freeview dev build here and give it a try:

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

Best,
Ruopeng


On Aug 28, 2015, at 11:23 AM, Matthieu Vanhoutte  
wrote:

> I can do it. Where could I send you these files ?
> 
> Best regards,
> 
> Matthieu
> 
> 2015-08-28 17:12 GMT+02:00 Ruopeng Wang :
> Would it be possible to send us lh.pial and lh.aparc.annot that caused the 
> crash?
> 
> Best,
> Ruopeng
> 
> On Aug 28, 2015, at 10:59 AM, Matthieu Vanhoutte 
>  wrote:
> 
>> I launched freeview, then added manually lh.pial and rh.pial of 
>> fsaverage_sym. A this point all is OK.
>> 
>> Then it crashed when I try to load graphically lh.aparc.annot or 
>> rh.aparc.annot. I viewed that in freesurfer mailing, this problem has been 
>> told in the beginning of 2014 but nothing afterthen.
>> 
>> Do you have a comman line way to manage to load annotation file under 
>> freeview ?
>> 
>> Matthieu
>> 
>> 2015-08-28 16:42 GMT+02:00 Douglas Greve :
>> what is your command line? Can you run it without the annotation?
>> 
>> 
>> On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote:
>>> Dear Freesurfer experts,
>>> 
>>> It seems impossible to load ?h.aparc.annot annotation file on ?h.pial 
>>> surface of the fsaverage_sym subject. When I try under freeview, it crashes 
>>> and gives me this error :
>>> 
>>> Did not find any volume geometry information in the surface
>>> pB Did not find any volume geometry information in the surface
>>> pB reading colortable from annotation file...
>>> colortable with 1036 entries read (originally 
>>> /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)
>>> [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 yakuza by matthieu Fri 
>>> Aug 28 11:32:19 2015
>>> [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
>>> 
>>> Could you help me please ?
>>> 
>>> Best regards,
>>> 
>>> Matthieu
>>> 
>>> 
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>>> Freesurfer@nmr.mgh.harvard.edu
>&g

Re: [Freesurfer] [FreeSurfer] Axis of Alignment

[Ruopeng Wang]

You can set the image semi-transparent and use the transformation tools on the 
Transform Volume window to align it with the reference image.

Ruopeng

> On Sep 23, 2015, at 5:22 PM, fmri  wrote:
> 
> how do you get all the image files to align with the one that you realign ?
> 
> On Aug 11, 2015, at 12:07 PM, Ruopeng Wang wrote:
> 
>> Hi Joseph,
>> 
>> In freeview you can use "Tools"->"Transform Volume" to reorient volumes.
>> 
>> Best,
>> Ruopeng
>> 
>> On 08/11/2015 02:59 PM, Bruce Fischl wrote:
>>> Ruopeng should be able to help you out
>>> 
>>> cheers
>>> Bruce
>>> On Tue, 11 Aug 2015, fmri wrote:
>>> 
>>>> Is there a wiki instruction block on how to reorient all volumes?
>>>> 
>>>> Thanks
>>>> 
>>>> On Aug 11, 2015, at 6:13 AM, Bruce Fischl wrote:
>>>> 
>>>>> Hi Joseph,
>>>>> 
>>>>> no it shouldn't matter to us what the angle is as long as it's in
>>>>> approximately the right orientation. You could reorient the volumes in
>>>>> freeview if you wanted, but I don't think it's necessary
>>>>> 
>>>>> cheers
>>>>> Bruce
>>>>> 
>>>>> 
>>>>> On Mon, 10 Aug 2015, fmri wrote:
>>>>> 
>>>>>> Hello FreeSurfer experts,
>>>>>> 
>>>>>> When MRI slices are not aligned to a more perfect plane of axis as shown 
>>>>>> in the 3D render attached. The sagittal slice is Not in-line with the 
>>>>>> midsagittal plane of the cerebral cortex.
>>>>>> 
>>>>>> All orthogonal slices are viewed in some Uneven angle, this is 
>>>>>> demonstrated in the Coronal image attached.
>>>>>> 
>>>>>> The coronal slice demonstrates the left hemisphere of the brain in view 
>>>>>> Before the right hemisphere.
>>>>>> 
>>>>>> This has become trouble some for editing and review purposes.
>>>>>> 
>>>>>> The greater concern is that we believe this could be affecting 
>>>>>> FreeSurfers' ability to distinguish critical areas in the temporal lobes.
>>>>>> 
>>>>>> Does the incorrect alignment of slices -to- brain anatomy matter when 
>>>>>> generating segmentations and parcellations?
>>>>>> 
>>>>>> If so is there a way to correct these angels before the recons begins to 
>>>>>> get better results in labeling segmentations and parcellations?
>>>>>> 
>>>>>> Or is there a way to correct these angles for viewing and editing 
>>>>>> purposes?
>>>>>> 
>>>>>> Any thoughts on the matter are appreciated,
>>>>>> 
>>>>>> Thanks so much,
>>>>>> 
>>>>>> Joseph
>>>>>> 
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>> 
>>>>> 
>>>>> The information in this e-mail is intended only for the person to whom it 
>>>>> is
>>>>> addressed. If you believe this e-mail was sent to you in error and the 
>>>>> e-mail
>>>>> contains patient information, please contact the Partners Compliance 
>>>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>>>> error
>>>>> but does not contain patient information, please contact the sender and 
>>>>> properly
>>>>> dispose of the e-mail.
>>>>> 
>>>> 
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Re: [Freesurfer] 3_group_comparison

[Ruopeng Wang]

Was the path of the overlay file correct? It looks like it can’t find the file. 
Try providing the full path of the overlay file in the freeview command.

Best,
Ruopeng

> On Sep 28, 2015, at 6:46 PM, Dusan Hirjak  wrote:
> 
> Many thanks!!!, yes, freeview has opened, but I am still not seeing any 
> results, just the "lh.inflated"
> 
> It says: "Failed to load surface overlay" 
> 
> and than I got the following message: 
> 
> bash-3.2$ freeview -f 
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> 2015-09-29 00:41:53.887 Freeview[22049:303] invalid drawable
> 2015-09-29 00:41:53.889 Freeview[22049:303] invalid drawable
> 2015-09-29 00:41:53.905 Freeview[22049:303] invalid drawable
> 2015-09-29 00:41:53.906 Freeview[22049:303] invalid drawable
> 2015-09-29 00:41:53.921 Freeview[22049:303] invalid drawable
> 2015-09-29 00:41:53.922 Freeview[22049:303] invalid drawable
> 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable
> 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable
> Did not find any volume geometry information in the surface
> ø;C 8Íÿ¿ø;C È+’Àá
> 
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> colortable with 36 entries read (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh,
>  -1): could not open file
> mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh,
>  -1): could not open file
> could not read overlay data from 
> /users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh
> mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh,
>  -1): could not open file
> 2015-09-29 00:42:02.445 Freeview[22049:303] modalSession has been exited 
> prematurely - check for a reentrant call to endModalSession:
> 
> I dont understand the problem. Do you have any ideas???
> 
> Thank you! 
> 
> Dusan
> 
> 
> 
> > To: freesurfer@nmr.mgh.harvard.edu 
> > From: gr...@nmr.mgh.harvard.edu 
> > Date: Mon, 28 Sep 2015 18:33:50 -0400
> > Subject: Re: [Freesurfer] 3_group_comparison
> > 
> > I think it needs a -f before the surface
> > 
> > On 09/28/2015 06:27 PM, Dusan Hirjak wrote:
> > > Many thanks, yes, it did work well.
> > >
> > > But, than I ran "freeview 
> > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5
> > >  
> > > -viewport 3d"
> > >
> > > and got the following message:
> > >
> > > bash-3.2$ freeview 
> > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5
> > >  
> > > -viewport 3d
> > >
> > > 2015-09-29 00:23:47.366 Freeview[22019:303] invalid drawable
> > >
> > > 2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable
> > >
> > > 2015-09-29 00:23:47.385 Freeview[22019:303] invalid drawable
> > >
> > > 2015-09-29 00:23:47.386 Freeview[22019:303] invalid drawable
> > >
> > > 2015-09-29 00:23:47.399 Freeview[22019:303] invalid drawable
> > >
> > > 2015-09-29 00:23:47.400 Freeview[22019:303] invalid drawable
> > >
> > > 2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable
> > >
> > > 2015-09-29 00:23:47.421 Freeview[22019:303] invalid drawable
> > >
> > > Unrecognized sub-option flag 'annot=aparc.annot'.
> > >
> > >
> > > Freeview has opened, but it showed no results at all:-(
> > >
> > >
> > > What should I do? I read that one has to upgrade the newest 
> > > freeview-version? Is it possible to get the newest version without 
> > > installing freesurfer again?
> > >
> > > Many thanks!
> > >
> > > Dusan
> > >
> > >
> > > 
> > > Date: Mon, 28 Sep 2015 11:35:50 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] 3_group_comparison
> > >
> > > Did you include the back slashes in your command? If so, remove them 
> > > and retry.
> > >
> > > On 9/25/15 7:11 PM, Dusan Hirjak wrote:
> > >
> > > Dear Freesurfer experts,
> > >
> > > I am trying to compare 3 groups (aut, sch, ges) according to
> > > thickness, area and LGI at once (omnibus test).
> > >
> > > I did run the following command:
> > >
> > > mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in
> > > thickness.fwhm15.fsaverage \ --target fsaverage --hemi lh \ --out
> > > lh.NSS_3_GR.thickness.15.mgh
> > >
> > >
> > > This step did work properly:-)
> > >
> > >
> > >
> > > Now, Im trying to run the follo

Re: [Freesurfer] FreeView updating

[Ruopeng Wang]

Latest freeview is just what comes with the developement version of
freesurfer. You can download the latest development verion from the
following page:

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



On 06/13/2016 12:44 PM, Chiu, Bryan (PHTH) wrote:

Hello,

I would like to download the latest version of FreeView so I could use 
the Recon Edit option. I've downloaded the latest version of 
FreeSurfer (v5.3), but it seems that I have an older version of 
FreeView (v1.0). Could someone please assist me in updating FreeView - 
I can't find the download for it.


Regards,
___
Bryan Chiu
Research Assistant
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy
Faculty of Medicine
University of British Columbia


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Re: [Freesurfer] swapped dimensions?

[Ruopeng Wang]

Would it be possible to send us a file?

Best,
Ruopeng

> On Jun 14, 2016, at 8:52 AM, Marja Caverlé  wrote:
> 
> Hi Bruce,
> 
> I did not get any error message, the page just remained empty after selecting 
> the files. Maybe my files were the reason why it didn't work.
> 
> Best,
> 
> Marja
> 
> On Tue, Jun 14, 2016 at 10:50 PM, Bruce Fischl  > wrote:
> freeview works fine with most dicoms. Do you get an error message?
> 
> On Tue, 14 Jun 2016, Marja Caverlé wrote:
> 
> Hi Bruce,
> 
> When I wanted to view them in freeview, simply nothing happened. Freeview
> did not load the files, so I assumed it did not work with dicoms, that's why
> I converted them.
> 
> Best,
> 
> Marja
> 
> On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve  >
> wrote:
>   What do you mean that FS did not accept the dicom files? Can you
>   provide a command line and terminal output? You can use
>   dcmunpack -src /path/to/dicom to get a list of the series in a
>   dicom folder
> 
>   On 6/13/16 9:57 PM, Marja Caverlé wrote:
>   Hi Bruce,
> 
>   I converted first of all because freesurfer did not accept
>   the dicom files. Furthermore the dicom's consist of a lot
>   of files of different scans, and they are not named
>   accordingly. The whole folder consists of files called eg
>   1254890234, so I have no clue how to get the right files.
> 
>   Thanks!
> 
> 
> 
> On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>   Hi Marja
> 
>   why are you converting at all? Why not just give one
>   of the dicom files in the correct series to
>   recon-all directly? I don't think we've ever seen an
>   orientation problem if you process that way
>   cheers
>   Bruce
> 
> 
>   On Tue, 14 Jun 2016, Marja Caverlé wrote:
> 
> No, when I view them in freeview the
> orientation is the same as in the
> original dicoms, but the results in the
> .stats files made me think that left
> and right might be swapped. Of course
> this could just really be the results
> of the correct hemispheres, but that is
> why I asked whether you are aware of
> any dimension switching during the
> recon-all. If not, than I can safely
> assume that the results are correct.
> 
> Best,
> 
> Marja
> 
> On Tue, Jun 14, 2016 at 1:29 AM, Bruce
> Fischl  >
> wrote:
>   so you convert from dicom to
> nifti, then view in freeview and
>   you think that the anatomical
> orientations are incorrect? That
>   should definitely not be the case
> 
>   On Tue, 14 Jun 2016, Marja Caverlé
> wrote:
> 
> Well the DICOMs I visualized
> in osiriX, and the
> niftis in both freesurfer
> and fsl. And there they
> seemed to match.
> So my question is; is there
> a possibility that
> dimensions are swapped
> during
> the recon -all? If not, then
> I am sure R=R and L=L.
> 
> Thanks!
> 
> On Tue, Jun 14, 2016 at
> 12:55 AM, Bruce Fischl
>  >
> wrote:
>   Hi Marja
> 
>   what did you visualize
> it in? I would suggest
> freeview
> 
>   cheers
>   Bruce
>   On Tue, 14 Jun 2016,
> Marja Caverlé wrote:
> 
> Hi Bruce,
> 
> I converted the
> images with MRIconvert,
> then I
> swapped them in
> FSL with
> swapdim.
> I checked the
> images by opening the
> original dicoms
> and the
> converted
> niftis, and then
> visually compared them
> (since the
> heads are not
> very
> symmetrical that
> was not too hard).
> 
> Best,
> 
> Marja
> 
> 
> On Tue, Jun 14,
> 2016 at 12:35 AM, Bruce
>

Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

Is there any other layer loaded? It looks like there is at least another 
overlay on top of the volume layer?

Best,
Ruopeng

> On Jun 23, 2016, at 2:37 PM, Ramtilak Gattu  wrote:
> 
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

That’s indeed strange. I wonder if it is a graphics card issue. Does the blue 
tone appear all the time? on any volume? 

> On Jun 23, 2016, at 3:31 PM, Ramtilak Gattu  wrote:
> 
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

So it happens with freeview all the time? Freeview uses openGL as backend for 
rendering, which I believe is not the case for fslview. Would it be possible 
for you to update your graphics card driver?

> On Jun 23, 2016, at 4:10 PM, Ramtilak Gattu  wrote:
> 
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

Is that all? Are there any other error messages?

On 06/24/2016 10:25 AM, Ramtilak Gattu wrote:


I tried updating my Nvidia drivers. but now whenever I try to open 
freeview it says " aborted ( core dumped).



please help.


Thanks


Regards

Tilak


*From:* Ramtilak Gattu
*Sent:* Thursday, June 23, 2016 5:27:12 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: freeview display problem

May be thats the problem. I'll try to give it a shot to see if it 
fixes the problem.



Thanks.


*From:* Ramtilak Gattu
*Sent:* Thursday, June 23, 2016 4:10:28 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: freeview display problem

This issue is only with freesurfer , images on fslview doesnt have 
this problem.





*From:* Ramtilak Gattu
*Sent:* Thursday, June 23, 2016 3:31:41 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: freeview display problem

That is just one layer the yellow contrast is from when we tune the 
contrast up or down.



*From:* Ramtilak Gattu
*Sent:* Thursday, June 23, 2016 2:37:36 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* freeview display problem

Hello ,


I am having strange freeview display problem. The images doesnt appear 
in gray scale anymore. Please have a look at the attachment.  Is there 
a switch that was  turned on that I am not aware of.



Could some one help.


Thanks


Regards
Tilak



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Re: [Freesurfer] visualizing statistical maps in FreeView

[Ruopeng Wang]

As to the color bar, would it be possible to send me a screenshot of it? 

Thanks,
Ruopeng

> On Jun 27, 2016, at 10:21 AM, Bruce Fischl  wrote:
> 
> Hi Lars
> 
> 
> I'll leave this for Ruopeng.
> 
> cheers
> Bruce
> 
> On Mon, 27 Jun 2016, Lars Morten Rimol wrote:
> 
>> Hi Bruce,
>>  
>> Yes, now it works (my guess is I loaded a single subject surface as template
>> before…) but I don’t find an FDR correction button in the Configure Overlay
>> interface. The fdr threshold can of course be calculated in Matlab but then
>> why not use tksurfer, which provides that functionality it in the
>> interface.  Also: Unlike in tksurfer, the color bar doesn’t seem to reflect
>> the thresholding of the overlay….
>>  
>>  
>> Thanks!
>>  
>> LMR
> ___
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Re: [Freesurfer] visualizing statistical maps in FreeView

[Ruopeng Wang]

Hi Lars,

Freeview currently does not have this feature. We will add it in the future.

Best,
Ruopeng

> On Jun 27, 2016, at 10:21 AM, Bruce Fischl  wrote:
> 
> Hi Lars
> 
> 
> I'll leave this for Ruopeng.
> 
> cheers
> Bruce
> 
> On Mon, 27 Jun 2016, Lars Morten Rimol wrote:
> 
>> Hi Bruce,
>>  
>> Yes, now it works (my guess is I loaded a single subject surface as template
>> before…) but I don’t find an FDR correction button in the Configure Overlay
>> interface. The fdr threshold can of course be calculated in Matlab but then
>> why not use tksurfer, which provides that functionality it in the
>> interface.  Also: Unlike in tksurfer, the color bar doesn’t seem to reflect
>> the thresholding of the overlay….
>>  
>>  
>> Thanks!
>>  
>> LMR
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

Do other colormaps (heat scale, jets, etc) look normal? 

> On Jun 28, 2016, at 2:01 PM, Ramtilak Gattu  wrote:
> 
> Hey Ruopeng,
> 
> I still couldnt figure out whats going on the freeview display. I updated the 
> Nvidia drivers but still its not displaying in gray scale.
> 
> please help.
> 
> thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 12:25:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> That is all . No error messages at all.
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 10:25:42 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> I tried updating my Nvidia drivers. but now whenever I try to open freeview 
> it says " aborted ( core dumped).
> 
> please help.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 5:27:12 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> May be thats the problem. I'll try to give it a shot to see if it fixes the 
> problem.
> 
> Thanks.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 4:10:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

This sounds very likely a video card/driver issue. Would it be possible for you 
any other program that uses OpenGL/vtk, such as 3D slicer, Paraview? How does 
glxgears command show? 

> On Jun 28, 2016, at 2:55 PM, Ramtilak Gattu  wrote:
> 
> Nope they dont look normal they are being displayed in some other colors like 
> heat is showing up as blue , jet as green etc. Even when the surfaces are 
> loaded up the color of the surfaces doesnt look right. when the surface 
> yellow is chosen are red it is being displayed as blue.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:01:00 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> Hey Ruopeng,
> 
> I still couldnt figure out whats going on the freeview display. I updated the 
> Nvidia drivers but still its not displaying in gray scale.
> 
> please help.
> 
> thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 12:25:50 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is all . No error messages at all.
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 10:25:42 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> I tried updating my Nvidia drivers. but now whenever I try to open freeview 
> it says " aborted ( core dumped).
> 
> please help.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 5:27:12 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> May be thats the problem. I'll try to give it a shot to see if it fixes the 
> problem.
> 
> Thanks.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 4:10:28 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

The color should be red, blue and green. It is your graphics card or graphics 
driver issue.

Best,
Ruopeng

> On Jun 28, 2016, at 3:46 PM, Ramtilak Gattu  wrote:
> 
> glxgears shows up a screen with three gear wheels in blue, pink and green and 
> frame information rate being printed out on the command window.
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:55:32 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> Nope they dont look normal they are being displayed in some other colors like 
> heat is showing up as blue , jet as green etc. Even when the surfaces are 
> loaded up the color of the surfaces doesnt look right. when the surface 
> yellow is chosen are red it is being displayed as blue.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:01:00 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> Hey Ruopeng,
> 
> I still couldnt figure out whats going on the freeview display. I updated the 
> Nvidia drivers but still its not displaying in gray scale.
> 
> please help.
> 
> thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 12:25:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> That is all . No error messages at all.
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 10:25:42 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> I tried updating my Nvidia drivers. but now whenever I try to open freeview 
> it says " aborted ( core dumped).
> 
> please help.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 5:27:12 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> May be thats the problem. I'll try to give it a shot to see if it fixes the 
> problem.
> 
> Thanks.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 4:10:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

Ok, you should try updating your graphics card driver. There is also chance 
that your graphics card is broken. Unfortunately we are not able to diagnose 
that for you. Sorry.

Best,
Ruopeng

> On Jun 28, 2016, at 4:17 PM, Ramtilak Gattu  wrote:
> 
> Attached is the screen shot comparison side by side.
> 
> I downloaded 3d slicer and even it dispalys images similar to what freeview 
> does. 
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 3:46:34 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> glxgears shows up a screen with three gear wheels in blue, pink and green and 
> frame information rate being printed out on the command window.
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:55:32 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> Nope they dont look normal they are being displayed in some other colors like 
> heat is showing up as blue , jet as green etc. Even when the surfaces are 
> loaded up the color of the surfaces doesnt look right. when the surface 
> yellow is chosen are red it is being displayed as blue.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:01:00 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> Hey Ruopeng,
> 
> I still couldnt figure out whats going on the freeview display. I updated the 
> Nvidia drivers but still its not displaying in gray scale.
> 
> please help.
> 
> thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 12:25:50 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is all . No error messages at all.
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 10:25:42 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> I tried updating my Nvidia drivers. but now whenever I try to open freeview 
> it says " aborted ( core dumped).
> 
> please help.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 5:27:12 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> May be thats the problem. I'll try to give it a shot to see if it fixes the 
> problem.
> 
> Thanks.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 4:10:28 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
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Re: [Freesurfer] Order of overlays

[Ruopeng Wang]

Hi Reza,

Right now in freeview aparc annotation is always drawn on top of 
overlays, just like in tkSurfer. I'll add an option draw it underneath 
the overlays.


Best,
Ruopeng

On 06/29/2016 10:09 AM, Bruce Fischl wrote:

Hi Reza

can you use freeview? We don't do any development on tksurfer and 
hardly use it anymore. Not sure if this is possible in freeview, I'll 
leave that for Ruopeng

cheers
Bruce
On Wed, 29 Jun 2016, Reza Rajimehr wrote:


Hi,
In Tksurfer, we want to show functional activity map and borders of 
aparc on
a surface. The borders of aparc are always drawn on top of the 
activity map,

which sometimes hide small activation blobs. Is it possible to draw the
activity map on top of the aparc borders?

Reza





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Re: [Freesurfer] Freeview question

[Ruopeng Wang]

Have you tried rebooting your computer?

Best,
Ruopeng

> On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote:
> 
> Hello FS Community,
> Lately, whenever I am trying to use freeview I get the following error
> message:
> 
> freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
> cannot open shared object file: No such file or directory
> Exit 127
> 
> The error started showing up after the cluster went down. I was wondering
> whether there was a way to fix this since I don't have admin privileges
> (and hence can't sudo).
> 
> Thanks in advance,
> Panos
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Re: [Freesurfer] significance overlay in freeview

[Ruopeng Wang]

Hi Caroline,

Are you running FS 5.3? The command on the webpage is based on the upcoming 
6.0, I believe. So some of the command line options are not available in 5.3.

Best,
Ruopeng

> On Jul 29, 2016, at 9:11 AM, Caroline Beelen  
> wrote:
> 
> Dear FS team,
>  
> Apologies in advance for perhaps again a rather basic question. I attempted 
> to load the aparc overlay in freeview by using the written command from the 
> group analysis page, however it failed to load correctly.  
>  
> I used the following command: 
> freeview -f 
> fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> è roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis 
> and dyslect is the contrast folder within this file (main effect of 
> dyslexia), containing a sig.mgh file (all seems fine)
>  
> Unfortunately, I got an error that it does not recognize 
> “overlay_treshold=4,5”. I used freeview –h and tried certain commands alike, 
> but they didn’t work. When leaving out this part, I got another error that it 
> failed to recognize “annot_outline=1”. Again, leaving this out too, freeview 
> loads itself and the DK-regions become visible. However, nothing else seems 
> to get activated, and even not when putting “configure overlay” (which is set 
> to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens. 
> When looking at the command line it says that it implemented the colortable 
> of DK-atlas (even twice), but it tells me nothing else. Also, after closing 
> and reloading Freeview by using the similar command and then clicking on 
> “configure overlay” the screen sometimes gets stuck, giving me the impression 
> that something must be wrong with the command.
>  
> Could you please help me out and provide me the right command-line for 
> loading the overlay of the significance map of 
> “roi.lh.area.dyslect_basic.glmdir/dyslect”?
>  
> Thanks in advance!
>  
> Kind regards, Caroline
>  
>  
>  
>  
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Re: [Freesurfer] mri_preproc error

[Ruopeng Wang]

Hi Younghoon,

You can adjust those settings from the GUI after you load the surface and 
overlays. Just click “Configure Overlay” button on the left panel after you 
load the overlay. 

Best,
Ruopeng

> On Aug 14, 2016, at 9:41 PM, YoungHoon Kwon  wrote:
> 
> Hello Freesurfer Developers,
> 
> I'm working on group analysis, and I have done GLM analysis(mris_glmfit) on 
> Linux. Next step is to visualize it, so I followed the instruction from the 
> FsTutorial website. 
> 
> freeview -f 
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> 
> Basically, I ran the commend above, and I got the effor "Unrecognized 
> sub-option flag 'annot_outline'" or "unrecognized sub-opton flag 
> 'overlay_threshold'." I think it's because I'm using old FS version which is 
> 5.1, and the tutorial is based on FS 6.1 version. I tried to use tksurfer, 
> but for some reason, it didn't work. I decided to use a freeview anyway.
> 
> On 5.1 version, what do I need to do to visualize them? How should I deal 
> with overlay threshold and annot_outline? Please let me know.
> 
> Best regards,
> Younghoon Kwon
> 
> 
> 2016-07-14 14:01 GMT-04:00 YoungHoon Kwon  >:
> 
> -- Forwarded message --
> From: YoungHoon Kwon mailto:yhk...@gmail.com>>
> Date: 2016-07-13 21:10 GMT-04:00
> Subject: mri_preproc error
> To: freesurfer@nmr.mgh.harvard.edu 
> 
> 
> Hello FreeSurfer Developers,
> 
> I tried to assemble the data by using mri_preproc, then it shows segmentation 
> fault (core dumped) after running. I searched for the solution, but I 
> couldn't find it.
> 
> Here's information
> 
> Error : Segmentation fault (core dumped)
> 
> Input : FS.txt (FSGD file)
> GroupDescriptorFile 1
> Title All
> Class Male
> Class Female
> Input002_S_4213_AMale
> Input002_S_4225_AMale
> Input002_S_4262_AFemale
> 
> command:
> [knho@in-rady-neuro11 test]$ mris_preproc --fsgd FS.txt \ --target fsaverage 
> --hemi lh \ --meas thickness \ --out practice_result.mgh
> nsubjects = 3
> tmpdir is ./tmp.mris_preproc.2677
> /localscratch3/test
> Log file is practice_result.mris_preproc.log
> Wed Jul 13 19:31:44 EDT 2016
> setenv SUBJECTS_DIR /localscratch3/test
> cd /localscratch3/test
> /net/age3/DATA_from_AGE0/FREESURFER/freesurfer51/bin/mris_preproc --fsgd 
> FS.txt --target fsaverage --hemi lh --meas thickness --out practice_result.mgh
> 
> Linux in-rady-neuro11.indyrad.iupui.edu 
>  3.16.2-201.fc20.x86_64 #1 SMP Mon 
> Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
> $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
> tmpdir is ./tmp.mris_preproc.2677
> Src lh sphere.reg
> Trg lh sphere.reg
> 
> ---
> #@# 1/3 002_S_4213_A Wed Jul 13 19:31:44 EDT 2016 --
> ---
> mri_surf2surf --srcsubject 002_S_4213_A --srchemi lh --srcsurfreg sphere.reg 
> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
> ./tmp.mris_preproc.2677/002_S_4213_A.1.mgh --sval 
> /localscratch3/test/002_S_4213_A/surf/lh.thickness --sfmt curv --noreshape 
> --no-cortex
> Segmentation fault (core dumped)
> 
> I found some advice from online, and it suggested to run recon-all; however 
> it didn't work. I really don't know what is wrong. Can anyone figure out this 
> error?
> 
> 1) Versioin : FreeSurfer 5.1
> 2) Platform : Linux
> 3) uname -a : Linux in-rady-neuro11.indyrad.iupui.edu 
>  3.16.2-201.fc20.x86_64 #1 SMP Mon 
> Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
> 
> 
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Re: [Freesurfer] error in manual edit by freeview

[Ruopeng Wang]

Would it be possible to send use the brain volume file?

Thanks,
Ruopeng

> On Aug 17, 2016, at 9:30 PM, 陈聪 <3110103...@zju.edu.cn> wrote:
> 
> Hi Doug
> Thank you for reply, My problem is shown in picture.
> Regards
> Cong
> 
> 
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Re: [Freesurfer] error in manual edit by freeview

[Ruopeng Wang]

Hi Cong,

It appears the brainmask you attached has an artifact slice for some reason. 
However I have no idea how it got there. Doug?

Best,
Ruopeng

> On Aug 18, 2016, at 10:19 PM, 3110103...@zju.edu.cn wrote:
> 
> Hi Doug and Ruopeng
>Can you receive pictures and brainmask.mgz file in attachment?  I don't 
> know why this slice mismatch with other slices,  other files such as T1 and 
> wm.mgz and other subjects works well. Thank you very much.
> 
> Regards
> Cong
> 
>> Date: Wed, 17 Aug 2016 10:49:35 -0400
>> From: Douglas Greve 
>> Subject: Re: [Freesurfer] error in manual edit by freeview
>> 
>> I'm not sure what you are describing. Can you send a picture?
>> 
>> 
>> On 8/17/16 8:42 AM, ?? wrote:
>>> Hi dear all
>>> I am using freeview to edit segmentation, I found one slice in coronal 
>>> view in brainmask.mgz mismatch with other slice, this slice obviously move 
>>> down.  WM and T1.mgz are normal, I don?t know how to move this wrong slice 
>>> back.  Any advice will be appreciated.
>>> 
>>> thanks very much.
>>> CONG
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Re: [Freesurfer] Freeview quits unexpectedly

[Ruopeng Wang]

Are you running FS 5.3 or the latest 6.0 beta? If former would it be possible 
for you to try 6.0 beta?

Best,
Ruopeng


> On Aug 19, 2016, at 1:27 PM, Corriveau-Lecavalier Nick 
>  wrote:
> 
> Hello FreeSurfer developers,
> 
> 
> I am trying to load a thickness file (ex: lh.long.thickness-avg.fwhm10.mgh) 
> in freeview, but as soon as I click the file or press enter after the command 
> line, the program quits unexpectedly. I can load T1, orig.mgz, .pial files, 
> etc. without problem. But when it comes to files that came out of the 
> long_mris_slopes command, freeview quits inevitably.
> 
> 
> Is it a problem with freesurfer or my computer (ex: graphic card not good 
> enough)? Do you have any idea why it keeps crashing? I am running a Macbook 
> Air mid 2013 with OS X El Captain, 1.3 GHz Intel Core i5, 4 GB 1600 Mhz DDR3, 
> Graphics: Intel HD Graphics 5000 1536 MB.
> 
> 
> Regards,
> 
> 
> Nick
> 
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Re: [Freesurfer] Freeview quits unexpectedly

[Ruopeng Wang]

BTW, what is the command you ran?

> On Aug 19, 2016, at 2:20 PM, Ruopeng Wang  wrote:
> 
> Are you running FS 5.3 or the latest 6.0 beta? If former would it be possible 
> for you to try 6.0 beta?
> 
> Best,
> Ruopeng
> 
> 
>> On Aug 19, 2016, at 1:27 PM, Corriveau-Lecavalier Nick 
>>  wrote:
>> 
>> Hello FreeSurfer developers,
>> 
>> 
>> I am trying to load a thickness file (ex: lh.long.thickness-avg.fwhm10.mgh) 
>> in freeview, but as soon as I click the file or press enter after the 
>> command line, the program quits unexpectedly. I can load T1, orig.mgz, .pial 
>> files, etc. without problem. But when it comes to files that came out of the 
>> long_mris_slopes command, freeview quits inevitably.
>> 
>> 
>> Is it a problem with freesurfer or my computer (ex: graphic card not good 
>> enough)? Do you have any idea why it keeps crashing? I am running a Macbook 
>> Air mid 2013 with OS X El Captain, 1.3 GHz Intel Core i5, 4 GB 1600 Mhz 
>> DDR3, Graphics: Intel HD Graphics 5000 1536 MB.
>> 
>> 
>> Regards,
>> 
>> 
>> Nick
>> 
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>> 
>> 
> 
> 
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Re: [Freesurfer] colour scale

[Ruopeng Wang]

There is a color bar button on the toolbar, or you can go to menu 
View->Show Color Scale.


Ruopeng

On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote:

Hi there

is there a way to view a colour scale bar in Freeview rather than 
Tksurfer, for instance, for a probability map? I can alter the Min and 
Max by "Configure Overlay" but cannot seem to display the bar next to 
my surface.


Many thanks

Trisanna


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




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Re: [Freesurfer] colour scale

[Ruopeng Wang]

It appears you are running version 5.3. The upcoming 6.0 should fix it.

> On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much 
>  wrote:
> 
> Hi there
> 
> yup, so I had seen that. The issue is it looks like this and doesn't seem to 
> change no matter what changes I make in the GUI (heat vs colour map, etc).
> 
> Best
> Trisanna
> 
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Mon, Sep 12, 2016 at 5:05 PM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> There is a color bar button on the toolbar, or you can go to menu View->Show 
> Color Scale.
> 
> Ruopeng
> 
> 
> On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote:
>> Hi there
>> 
>> is there a way to view a colour scale bar in Freeview rather than Tksurfer, 
>> for instance, for a probability map? I can alter the Min and Max by 
>> "Configure Overlay" but cannot seem to display the bar next to my surface.
>> 
>> Many thanks
>> 
>> Trisanna
>> 
>> 
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>> 
>> 
>> 
>> 
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Re: [Freesurfer] hide colored slices in 3d view?

[Ruopeng Wang]

Hi Jessica,

There is no such command-line option in version 5.3. Sorry.

Ruopeng

> On Sep 16, 2016, at 10:44 AM, j.oschw...@psychologie.uzh.ch wrote:
> 
> 
> Hi Freesurfer users,
> 
> I wrote a script to automatize taking screenshots in Freeview. Unfortunately, 
> in the 3d view the colored slices are automatically included in the picture.  
> Is there a way to hide them? I am using the current 5.3 version of 
> Freesurfer. 
> I know that the development build includes this option (-hide-3d-slices), but 
> I cannot access the FTP server right now to download it. Is there probably 
> also a command in the version I am currently using? 
> 
> Best
> Jessica
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

Is there any error message on the terminal? What happens if you run “glxgears” 
command? Does it run?

Best,
Ruopeng

> On Sep 23, 2016, at 4:35 PM, KALEY E ELLIS  wrote:
> 
> Hello FreeSurfer Developers,
> 
> I am attempting to open freeview to view the brainmask on a subject in our 
> study. Everything looks normal, except there is no image displayed (see 
> attachment). Could you please let me know how I can fix this?
> 
> Thank you,
> Kaley
> 
> Associate Research Specialist
> Center for Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
>  PM.png>___
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Re: [Freesurfer] Freeview Loading Volumes

[Ruopeng Wang]

Hi Bob,

I think  freeview by default automatically locates to the default mri 
directory under the current subject. It is convenient in some use case 
but apparently not so much in your case. I will make that optional or 
figure out a better way to handle this.

Best,
Ruopeng

On 9/25/2016 9:46 AM, Robert Kraft wrote:
> I use Freeview on a daily basis as my primary image viewer.  I like it a lot 
> and found it to be tremendously useful. I am usually interested in opening 
> images in the current directory where I launched Freeview from the command 
> line.  I know you can load multiple images at once from the command line but 
> occasionally I want to load an additional image. Ideally, I would like 
> Freeview when I want to load a volume to open up the file explorer tool in 
> the current directory.  Instead, it opens up in another directory and I have 
> to click down several directories before finding the file that I want.  
> Freeview has been consistently opening up in the same directory.  I just 
> can’t figure out why it picks that directory.
>
> If someone could tell me if it is possible for Freeview to open the file 
> browser in the directory it was launched I would be extremely grateful.
>
> Thanks for your help in advance,
>
> Bob
>
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Re: [Freesurfer] FreeView questions

[Ruopeng Wang]

Hi Anders,

Try turn off/on color bar or change the overlay thresholds to see if it 
updates. I believe this is fixed in v6.0. As to rotate the 3D view by 
certain degrees, there is no GUI for that. You can do that in the 
command-line via "-cam" options. Run "freeview -h" for more info on how 
to use it.


Best,
Ruopeng

On 10/05/2016 11:40 AM, Anders Hougaard wrote:

Dear all,

Please see the attached image of a surface overlay (gamma.mgh from a 
standard group analysis of cortical thickness with two groups and two 
contrasts).

Any ideas why the color bar looks weird?

Question 2: How do you specify rotation in 3D view like it was 
possible in TKsurfer, e.g. if I want to rotate the 3D brain exactly 45 
degress clockwise around the z axis?


Thank you :)

Best,
Anders


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Re: [Freesurfer] how to edit the cortex label by adding vertecies

[Ruopeng Wang]

No, it is not supported in freeview yet.

Ruopeng

> On Nov 3, 2016, at 10:05 AM, Bruce Fischl  wrote:
> 
> Hi Linn
> 
> sure, you can edit the label directly. This might not be supported yet in 
> freeview (Ruopeng: is it?) in which case you have to use tksurfer.
> 
> The other (and probably better) alternative is to figure out why the label is 
> incorrect and edit the underlying cause. In the occipital lobe this is 
> usually because the occipital horn of the ventricle incorrectly extends into 
> the calcarine. You can fix this by editing the aseg to relabel those voxels 
> as unknown and rerunning recon-all from their forward.
> 
> cheers
> Bruce
> 
> 
> On Thu, 3 Nov 2016, l.c.b.nor...@psykologi.uio.no wrote:
> 
>> Hello Freesurfer Developers,
>> 
>> I want to add vertecies to the cortex label as certain vertecies in the
>> occipital lobe is wrongfully segmented as medial wall. Is there a way to
>> do this?
>> 
>> Thank you in advance!
>> 
>> Cheers,
>> Linn
>> 
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Re: [Freesurfer] grayscale display turns red in freeview

[Ruopeng Wang]

You need to adjust the color scale. Click on “Configure Overlay” button to 
adjust it.

Best,
Ruopeng

> On Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu  
> wrote:
> 
> Hi
> 
> Am having a bit of a problem that may be easy to resolve.
> 
> I want to view an LGI two-group comparison I did in mri glm-fit with 
> freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mg 
> h). The grayscale inflated surface 
> turns red like what is in picture-1
> 
> Please have anyone an idea why this is happening and what I can do to change 
> it back to grayscale like picture 2
> Thanks for your help
> 
> Emmanuel
> 
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Re: [Freesurfer] grayscale display turns red in freeview

[Ruopeng Wang]

What happens when you click on the button? 

> On Nov 21, 2016, at 9:02 AM, Emmanuel Nwosu  
> wrote:
> 
> Thanks Ruopeng. I can't open the configure overlay button. Is there any other 
> means of changing it? 
> 
> On Mon, Nov 21, 2016 at 3:58 PM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> You need to adjust the color scale. Click on “Configure Overlay” button to 
> adjust it.
> 
> Best,
> Ruopeng
> 
>> On Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu > <mailto:emmanuel.c.nw...@gmail.com>> wrote:
>> 
>> Hi
>> 
>> Am having a bit of a problem that may be easy to resolve.
>> 
>> I want to view an LGI two-group comparison I did in mri glm-fit with 
>> freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mg 
>> <http://cache.th13.abs.sig.cluster.mg/>h). The grayscale inflated surface 
>> turns red like what is in picture-1
>> 
>> Please have anyone an idea why this is happening and what I can do to change 
>> it back to grayscale like picture 2
>> Thanks for your help
>> 
>> Emmanuel
>> 
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Re: [Freesurfer] grayscale display turns red in freeview

[Ruopeng Wang]

Can you post a screenshot? Are you running freeview remotely?

> On Nov 21, 2016, at 9:32 AM, Emmanuel Nwosu  
> wrote:
> 
> it opens a blank "configure overlay" dialog, then the screen goes dark
> 
> On Mon, Nov 21, 2016 at 4:29 PM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> What happens when you click on the button? 
> 
>> On Nov 21, 2016, at 9:02 AM, Emmanuel Nwosu > <mailto:emmanuel.c.nw...@gmail.com>> wrote:
>> 
>> Thanks Ruopeng. I can't open the configure overlay button. Is there any 
>> other means of changing it? 
>> 
>> On Mon, Nov 21, 2016 at 3:58 PM, Ruopeng Wang > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>> You need to adjust the color scale. Click on “Configure Overlay” button to 
>> adjust it.
>> 
>> Best,
>> Ruopeng
>> 
>>> On Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu >> <mailto:emmanuel.c.nw...@gmail.com>> wrote:
>>> 
>>> Hi
>>> 
>>> Am having a bit of a problem that may be easy to resolve.
>>> 
>>> I want to view an LGI two-group comparison I did in mri glm-fit with 
>>> freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mg 
>>> <http://cache.th13.abs.sig.cluster.mg/>h). The grayscale inflated surface 
>>> turns red like what is in picture-1
>>> 
>>> Please have anyone an idea why this is happening and what I can do to 
>>> change it back to grayscale like picture 2
>>> Thanks for your help
>>> 
>>> Emmanuel
>>> 
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>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Re: [Freesurfer] grayscale display turns red in freeview

[Ruopeng Wang]

This is likely due to remote display. Would it be possible for you to run it 
locally? You can also adjust overlay settings from the command-line, although 
it is not as convenient as the GUI. Run “freeview -h” and look for surface 
overlay related options. 

> On Nov 21, 2016, at 9:48 AM, Emmanuel Nwosu  
> wrote:
> 
> Yes am running it on a remote server. Here is the screen shot
> 
> On Mon, Nov 21, 2016 at 4:40 PM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> Can you post a screenshot? Are you running freeview remotely?
> 
>> On Nov 21, 2016, at 9:32 AM, Emmanuel Nwosu > <mailto:emmanuel.c.nw...@gmail.com>> wrote:
>> 
>> it opens a blank "configure overlay" dialog, then the screen goes dark
>> 
>> On Mon, Nov 21, 2016 at 4:29 PM, Ruopeng Wang > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>> What happens when you click on the button? 
>> 
>>> On Nov 21, 2016, at 9:02 AM, Emmanuel Nwosu >> <mailto:emmanuel.c.nw...@gmail.com>> wrote:
>>> 
>>> Thanks Ruopeng. I can't open the configure overlay button. Is there any 
>>> other means of changing it? 
>>> 
>>> On Mon, Nov 21, 2016 at 3:58 PM, Ruopeng Wang >> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
>>> You need to adjust the color scale. Click on “Configure Overlay” button to 
>>> adjust it.
>>> 
>>> Best,
>>> Ruopeng
>>> 
>>>> On Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu >>> <mailto:emmanuel.c.nw...@gmail.com>> wrote:
>>>> 
>>>> Hi
>>>> 
>>>> Am having a bit of a problem that may be easy to resolve.
>>>> 
>>>> I want to view an LGI two-group comparison I did in mri glm-fit with 
>>>> freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mg 
>>>> <http://cache.th13.abs.sig.cluster.mg/>h). The grayscale inflated surface 
>>>> turns red like what is in picture-1
>>>> 
>>>> Please have anyone an idea why this is happening and what I can do to 
>>>> change it back to grayscale like picture 2
>>>> Thanks for your help
>>>> 
>>>> Emmanuel
>>>> 
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>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>> 
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>>> 
>>> 
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Re: [Freesurfer] V6 beta freeview - stopped loading remaining files when one is missing

[Ruopeng Wang]

I will add a "-continue" option for this. It may not make it to the 
final V6 release. But you can always download our nightly dev build of 
freeview anytime.


Best,
Ruopeng

On 01/04/2017 03:38 PM, Antonin Skoch wrote:

Dear experts,

with V6 beta version of freeview I encountered, that when some input 
file specified in command line is missing, the loading of remaining 
files is stopped. This was not the case with 5.3 version. I found this 
feature handy. Do you think that it would be good to implement this 
behavior also for V6 version of freeview?


Regards,

Antonin Skoch



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Re: [Freesurfer] Problem with freeview

[Ruopeng Wang]

I’m not sure about the first part of the message, but "Did not find any volume 
geometry information in the surface” can be ignored. It is just a warning. Did 
the program still run? If so, you can ignore these warnings.

Best,
Ruopeng

> On Jan 4, 2017, at 6:49 PM, Jennifer Szeto  wrote:
> 
> Hi Freesurfer Experts, 
>  
> I have installed Freesurfer5.3 and it seems to be working fine. However when 
> i tried to load up the GLM analysis (after doing mris_preproc and mri_glmfit) 
> results on freeview, i got the following message: 
>  
> "OpenGL warning: No pincher, please call crStateSetCurrentPointers () in your 
> SPU Did not find any volume geometry information in the surface" 
>  
> Just wondering if anyone knows the solution to this? 
>  
> Thanks for your help!
>  
> Jen
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Re: [Freesurfer] Control points displaying differently in freeview as opposed to tkmedit

[Ruopeng Wang]

Would it be possible to send us the volume and control point files?

Thanks,
Ruopeng

On 09/25/2013 02:09 PM, Jonathan Holt wrote:
> I've read in the mailing list archives people have had issues with tkmedit 
> and free view displaying control points differently. For me the first brain 
> I've loaded up has a single control point in free view that does not show in 
> tkmedit. Others have complained of free view showing points seemingly at 
> random? Is this a user related issue perhaps?
>
> Here are the contents of the control.dat file in question
>
> 55.00 -60.00 -41.00
> 54.00 -61.00 -41.00
> 53.00 -62.00 -41.00
> 52.00 -59.00 -37.00
> 52.00 -63.00 -40.00
> 2.00 48.00 14.00
> 2.00 47.00 13.00
> 1.00 46.00 11.00
> 1.00 41.00 8.00
> 1.00 40.00 6.00
> 0.00 45.00 10.00
> 0.00 44.00 10.00
> 0.00 43.00 10.00
> 0.00 39.00 6.00
> 0.00 38.00 6.00
> 0.00 37.00 7.00
> -1.00 42.00 10.00
> info
> numpoints 17
> useRealRAS 0
>
>
> the errant control point is on slice 128 best viewed coronally.
>
> jon
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Re: [Freesurfer] Freeview questions

[Ruopeng Wang]

Hi Jon,

1) No, there is no way to do that in freeview.

2) In Editing mode, you can use shift+ctrl+Left mouse button to move the 
cursor.

Ruopeng

On 10/01/2013 12:50 PM, Jonathan Holt wrote:
> Simply to make sure,
>
> 1) Is there no way that one can edit two volumes simultaneously similarly to 
> tkmedits aux+main volume brush?
>
> 2) When editing voxels in freeview, is there anyway to have the cursor behave 
> the same way it does in navigation mode. That is, I'd like to be able to see 
> exactly where I'm editing in all 3 views, rather than just the one I'm 
> editing in.
>
> Best,
> Jon
>
>
>
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Re: [Freesurfer] Freeview Volume & Surface alignment

[Ruopeng Wang]

Would it be possible to send us the command line and the files that produces 
the screenshot?

Thanks,
Ruopeng

On Oct 16, 2013, at 2:28 PM, Kambiz Tavabi  wrote:

> I would like to inspect the results of my surface boundary on the volume as 
> per the approach in tkmedit. However in freeview the surface boundary and 
> volume are not aligned in a common space. Why is that? How does one go about 
> aligning the tkregRAS with the RAS? (those are apparently the two different 
> coordinate systems according to the information panel). Thanks in advance.
> 
> 
> 
> Kambiz Tavabi PhD
> Institute for Learning & Brain Sciences
> 1715 Columbia Road N
> Portage Bay Building
> Box 357988
> University of Washington
> Seattle, WA 98195-7988
> Tel: 206-685-6173
> 
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Re: [Freesurfer] Freeview Volume & Surface alignment

[Ruopeng Wang]

Hi Kambiz,

It would still be very helpful if you could send us the volume and the surface 
files so that we can investigate.

Thanks,
Ruopeng

On Oct 16, 2013, at 4:10 PM, Kambiz Tavabi  wrote:

> Hi Ruopeng,
> Sorry for the confusion in my initial post. The screen capture is actually a 
> grab from one of the viewing windows in FREEVIEW; so I am actually not doing 
> anything on the command line with tkmedit. In freeview, I am loading the 
> original T1 volume and then loading the skin, outer skull, or inner skull 
> surfaces from the watershed algorithm and they are obviously in different 
> coordinates. As a matter of fact the exact same volume and surface boundary 
> load up perfectly lined up in tkmedit. I am just wondering why the two 
> programs do not behave in the same way, and how I can get them to behave 
> similarly if possible. -Kambiz
> 
> 
> Kambiz Tavabi PhD
> Institute for Learning & Brain Sciences
> 1715 Columbia Road N
> Portage Bay Building
> Box 357988
> University of Washington
> Seattle, WA 98195-7988
> Tel: 206-685-6173
> ----
> 
> 
> On Wed, Oct 16, 2013 at 12:26 PM, Ruopeng Wang  
> wrote:
> Would it be possible to send us the command line and the files that produces 
> the screenshot?
> 
> Thanks,
> Ruopeng
> 
> On Oct 16, 2013, at 2:28 PM, Kambiz Tavabi  wrote:
> 
>> I would like to inspect the results of my surface boundary on the volume as 
>> per the approach in tkmedit. However in freeview the surface boundary and 
>> volume are not aligned in a common space. Why is that? How does one go about 
>> aligning the tkregRAS with the RAS? (those are apparently the two different 
>> coordinate systems according to the information panel). Thanks in advance.
>> 
>> 
>> 
>> Kambiz Tavabi PhD
>> Institute for Learning & Brain Sciences
>> 1715 Columbia Road N
>> Portage Bay Building
>> Box 357988
>> University of Washington
>> Seattle, WA 98195-7988
>> Tel: 206-685-6173
>> 
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> 
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
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> at
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Re: [Freesurfer] freeview "invalid drawable"

[Ruopeng Wang]

You can just ignore this warning message on Mac. 

Best,
Ruopeng

On Oct 23, 2013, at 8:52 PM, Elissa McIntosh  wrote:

> Hi, When trying freeview command (see below) from the “Testing your 
> freesurfer installation” page using my own data, freesurfer opened, but I am 
> concerned about the “invalid drawable” lines. The message happened when I ran 
> this command on the "bert" data too. What does invalid drawable mean? 
> 
>  
> [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview 
> -v $SUBJECTS_DIR/ABU/mri/norm.mgz -v 
> $SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
> $SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f 
> $SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow -f 
> $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f 
> $SUBJECTS_DIR/ABU/surf/rh.pial:annot=aparc:edgecolor=red
> 
> 2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable
> 
> 2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable
> 
> 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable
> 
> 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable
> 
> 2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable
> 
> 2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable
> 
> 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable
> 
> 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable
> 
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> colortable with 36 entries read (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> colortable with 36 entries read (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> 
> 
> Thank you,
> Elissa 
> 
> 
> 
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Re: [Freesurfer] Freeview

[Ruopeng Wang]

Hi Lindsay,

I think there was no such option to display multiple surface labels at 
once even in the old version. However, we will add it in the future.


Best,
Ruopeng

On 10/28/2013 01:48 PM, Lindsay Squeglia wrote:

Hi all,

I recently updated to FreeSurfer version 5.3.0, and I am now having 
problems with freeview that I didn't  have on the older versions. When 
I go to "Surfaces" and "Load Labels", it only shows one label at a 
time. Previously, I could add several labels and all would appear on 
the Figure. Does anyone know a fix for this?


Thanks!
Lindsay




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Re: [Freesurfer] Freeview

[Ruopeng Wang]

Was that from freeview or tksurfer?

On 10/28/2013 02:06 PM, Lindsay Squeglia wrote:

Hi Ruopeng,

Thanks for your response! I used to do it all the time in the previous 
versions of FreeSurfer (see attached). I am not sure why the new 
version is different.


Thanks!
Lindsay




On Mon, Oct 28, 2013 at 11:01 AM, Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>> wrote:


Hi Lindsay,

I think there was no such option to display multiple surface
labels at once even in the old version. However, we will add it in
the future.

Best,
Ruopeng


On 10/28/2013 01:48 PM, Lindsay Squeglia wrote:

Hi all,

I recently updated to FreeSurfer version 5.3.0, and I am now
having problems with freeview that I didn't  have on the older
versions. When I go to "Surfaces" and "Load Labels", it only
shows one label at a time. Previously, I could add several labels
and all would appear on the Figure. Does anyone know a fix for this?

Thanks!
Lindsay




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Re: [Freesurfer] Fwd: freeview error

[Ruopeng Wang]

Hi Rujing,

Your hardware setup does sound a bit insufficient to run freeview smoothly. But 
I don't think that is the reason "configure overlay" hangs. Would it be 
possible to send us the files used in your command? 

Best,
Ruopeng

On Dec 31, 2013, at 1:04 AM, rujing cha  wrote:

> Hi Bruce and others,
> Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and
> setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz,
> and I setup the nvidia drivers completely. Then I tried to run this
> command:
> freeview -f 
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
> . It did present the underlay(lh.inflated),overlay and annot, but it
> suspended when I click the button "configure overlay". Then freeview
> were suspended. The CPU ran "100%",and memory ran "23%". There was
> nothing to do but terminated it manually in the command console by
> "ctrl + c".
> I want to know why I cannot configure overlay. Is it a poor graphic
> card or CPU or memory? My graphic card is "NVIDIA GeForce 8600 GT",
> and CPU is "Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz", and
> RAM is 2.00G.
> Thanks Bruce and others.
> All the best.
> 2013-12-30
> 
> 
> 
> Rujing Zha
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Re: [Freesurfer] problems about freeview

[Ruopeng Wang]

Hi Rujing,

I am able to replicate the issue with 5.3.0 release. The good news is the issue 
does not appear in the current dev version (so I think it has been fixed). 
Zeke, would it be possible for Rujing to download a copy of the latest freeview 
build?

Best,
Ruopeng

On Jan 4, 2014, at 10:40 AM, "charujing"  wrote:

> Dear doug, bruce and others,
> Previously I could not view "
> freeview -f 
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
> " from the 
> "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis";. The 
> freeview did represent 3 images. But it reported a something about no 
> geomatric information and I couldnot configure the overlay(When I clicked the 
> "configure overlay", it stopped without any response). My OS is CentOS 6.5 
> desktop version, and graphic card is NVIDIA GEFORCE GTX 650 and setup the 
> NVIDIA driver. Freesurfer version is 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has 2G 
> memory and 4 processors.
> I need help to fix it.
> If anyone have viewed sample data or other data(*.inflated, 
> *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by freeview 
> just as above, would you please tell me some information? The information I 
> need is Freesurer version, Centos version(desktop or others) and something in 
> CentOS setup, graphic card version and its driver, memory size.
> Thanks very much, doug, brucen and others.
> Any reply will be highly appreciated.
> All the best.
> Rujing Zha 
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Re: [Freesurfer] Freeview Save and Go-to Point Issue

[Ruopeng Wang]

Would it be possible to share the data that shows this issue? Or does it 
happen to any volume you are viewing with freeview?

Ruopeng


On 01/27/2014 12:47 PM, Denker, Alexander (NIH/NIMH) [F] wrote:
> I was strictly using the freeview GUI and not tksurfer so I didn¹t notice
> any error messages.
>
>
> Alexander
>
> On 1/27/14, 12:10 PM, "Bruce Fischl"  wrote:
>
>> Hi Alexander
>>
>> do you see any error messages in the terminal window where you started
>> tksurfer?
>>
>> Bruce
>>
>>
>> On Mon, 27 Jan 2014, Denker,
>> Alexander (NIH/NIMH) [F] wrote:
>>
>>> Hi,
>>>
>>> I am experiencing an issue where I try to save a point in an inflated
>>> brain view and go to the saved point on my brainmask/wm volume and the
>>> point is jumping to a space off of the brain. This happens consistently.
>>> Am I doing something wrong or is this a bug?
>>>
>>> Thank you,
>>> Alexander
>>>
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>>>
>>
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Re: [Freesurfer] freeview porblem under ubuntu 12.04

[Ruopeng Wang]

Can you post a screenshot?

Ruopeng

On 01/30/2014 12:58 PM, Markus Gschwind wrote:

Dear Experts,

I have installed Freesurfer 5.3 under ubuntu 12.04.

It is running fine except for Freeview which is causing heavy graphic 
trouble (thousands of colored squares in the black fields where the 
brains should be displayed.


Tksurfer is working fine.

Glxgears is showing the rotating blue, red and green gears.

There is no error in the terminal.

What could I do to track down the problem?

Thanks for help!
Markus


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Re: [Freesurfer] freeview porblem under ubuntu 12.04

[Ruopeng Wang]

This looks like graphics driver issue. Is your graphics card driver 
up-to-date? Is there any error/warning message in the console?


Ruopeng

On 01/30/2014 01:17 PM, Markus Gschwind wrote:

HI Ruopeng,

Here it is.

Is it related to the tbouble shoot I did for trackvis?

Thanks for having a look,
Markus


2014-01-30 Ruopeng Wang <mailto:rpw...@nmr.mgh.harvard.edu>>


Can you post a screenshot?

Ruopeng


On 01/30/2014 12:58 PM, Markus Gschwind wrote:

Dear Experts,

I have installed Freesurfer 5.3 under ubuntu 12.04.

It is running fine except for Freeview which is causing heavy
graphic trouble (thousands of colored squares in the black fields
where the brains should be displayed.

Tksurfer is working fine.

Glxgears is showing the rotating blue, red and green gears.

There is no error in the terminal.

What could I do to track down the problem?

Thanks for help!
Markus


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Re: [Freesurfer] Color Bar options

[Ruopeng Wang]

Hi Jon,

The range of color bar is automatically set by the internal color bar 
component that is used to display it. There is no option to change it at 
this point. I'll take note on that for future update.

Best,
Ruopeng

On 02/10/2014 11:49 AM, Jonathan Holt wrote:
> Hi all,
>
> Would someone kindly point me toward color bar options, specifically for 
> thickness maps. The color bar that appears by default includes negative 
> values, and the bit with positive thickness values is very compressed.
>
> For reference I’m looking at surfaces in freeview brought up by
>
> freeview -f 
> SUBJ_ID/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
>
>
> jon
>
>
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Re: [Freesurfer] Erasing, adding voxels in Freeview

[Ruopeng Wang]

Hi Alexander,

Eraser value is used for erasing. Brush value is used for drawing. To 
erase, just hold shift key and press left mouse button.

Best,
Ruopeng

On 02/10/2014 10:23 AM, Denker, Alexander (NIH/NIMH) [F] wrote:
> Hi all,
>
> This is probably a very elementary error in my use of Freeview, but I have 
> been having trouble adding voxels to scans. I set the eraser value to "0", 
> but when I draw, the voxel still shows up as a black box instead of grey. Am 
> I not setting the right values or am I just in the wrong viewing mode?
>
> Thanks!
> Alexander
>
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Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

[Ruopeng Wang]

You can load surface-based time course data as a surface overlay, I believe. 
But there is no function to view the scatter plot. The time course window is 
for volume only.

Ruopeng

On Feb 26, 2014, at 10:13 PM, Douglas Greve  wrote:

> 
> That command definitely will not work. When you ran the command I sent, did 
> it at least show you something on the surface? 
> 
> Ruopeng, is there a way to load a surface-based timecourse in freeview?
> 
> doug
> 
> 
> 
> 
> On 2/26/14 9:11 PM, charujing123 wrote:
>> Hi doug,
>> Thanks doug.
>> I am sorry to describe my question no very clearly.It did work,but I want to 
>> view time course of lh.score.thickness.00.mgh vertex by vertex. So I need to 
>> try -v option to view time course manually as you just told me. However I 
>> cannot view anything but darkness when I try ""freeview -v 
>> lh.score.thickness.00.mgh"". Is there any tool or method to present a time 
>> course window(or a colume of numbers) when I click one voxel or vertex. And 
>> numbers in time course window will change when I click other voxel or vertex.
>> Thanks,
>> All the best.
>> Rujing Zha
>>  
>> 2014-02-27
>> charujing123
>> 发件人：Douglas N Greve 
>> 发送时间：2014-02-27 01:51
>> 主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
>> 收件人："freesurfer"
>> 抄送：
>>  
>> Try this 
>> freeview -f  
>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
>>  
>> Don't use -v in this case because -v is for a volumes and volume  
>> overlays and all your data are surface overlays 
>>  
>>  
>> On 02/25/2014 08:38 PM, charujing123 wrote: 
>> > Hi doug and others, 
>> > It will be highly appreciated,if anyone can help me. 
>> > Thanks. 
>> > All the best. 
>> > Rujing Zhas 
>> > 2014-02-26 
>> >  
>> > charujing123 
>> >  
>> > *发件人：*"charujing123" 
>> > *发送时间：*2014-02-25 12:01 
>> > *主题：*Re: [Freesurfer] time course in mri_info  
>> > lh.gender_age.thickness.10.mgh 
>> > *收件 人：*"freesurfer@nmr.mgh.harvard.edu" 
>> > *抄送：* 
>> > Hi doug, 
>> > When I try to do this by "freeview -f  
>> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
>> >   
>> > -v lh.score.thickness.00.mgh" or "freeview -v  
>> > lh.score.thickness.00.mgh", it did create a window of time course.  
>> > However there is nothing in the freeview window except  
>> > darkness((i.e.fig1 in the attachment)). By the way, I can see  
>> > something by "freeview -f  
>> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh"(i.e.fig2
>> >   
>> > in the attachment). All of these can be got in the attachment. 
>> > Thanks. 
>> > All the best. 
>> > Rujing Zha 
>> > 2014-02-25 
>> >  
>> > charujing123 
>> >  
>> > *发件人：*"charujing123" 
>> > *发送时间：*2014-02-25 10:28 
>> > *主题：*Re: [Freesurfer] time course in mri_info  
>> > lh.gender_age.thickness.10.mgh 
>> > *收件 人：*"freesurfer@nmr.mgh.harvard.edu" 
>> > *抄送：* 
>> > Thanks doug 
>> > All the best. 
>> > Rujing Zha 
>> > 2014-02-25 
>> >  
>> > charujing123 
>> >  
>> > *发件 人：*Douglas N Greve  
>> > *发送时间：*2014-02-25 00:31 
>> > *主题：*Re: [Freesurfer] time course in mri_info  
>> > lh.gender_age.thickness.10.mgh 
>> > *收件 人：*"freesurfer" 
>> > *抄送：* 
>> > On 02/23/2014 08:32 PM, charujing123 wrote: 
>> > > Hi all, 
>> > > I have two questions. 
>> > > 1,If I want to get the value of specific voxel from the 
>> > > lh.gender_age.thickness.10.mgh, which code can I use to perform it? 
>> > You can go to that vertex when you have it loaded into FreeView, 
>> > otherwise you can load it into matlab (MRIread.m). Make sure to account 
>> > for the fact that matlab uses 1-based indices whereas FS uses 0-based. 
>> > > 2,How to graph the time course of specfic voxel from the 
>> > > lh.gender_age.thickness.10.mgh by freeview? 
>> > Add "-v lh.gender_age.thickness.10.mgh" to your freeview command line 
>> > > Thanks. 
>> > > All the best. 
>> > > Rujing Zha 
>> > > 2014-02-24 
>> > >  
>> >  
>> > > charujing123 
>> > > 
>> > > 
>> > > ___ 
>> > > Freesurfer mailing list 
>> > > Freesurfer@nmr.mgh.harvard.edu 
>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> > --  
>> > Douglas N. Greve, Ph.D. 
>> > MGH-NMR Center 
>> > gr...@nmr.mgh.harvard.edu 
>> > Phone Number: 617-724-2358 
>> > Fax: 617-726-7422 
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
>> > FileDrop: https://gate.nmr.mgh.harvard.ed

Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

[Ruopeng Wang]

I have added support to display surface-based timecourse data in Time 
Course window. It should be available in the dev build tomorrow.


Ruopeng

On 02/27/2014 12:17 AM, charujing123 wrote:

Hi doug and Ruopeng,
Thanks doug.
The command you sent did show something on the surface, but the button 
of "show time course" can not be clicked.

Thanks doug and ruopeng.
All the best.
Rujing Zha
2014-02-27

charujing123

*发件人：*Douglas Greve 
*发送时间：*2014-02-27 11:13
*主题：*Re: [Freesurfer] time course in mri_info 
lh.gender_age.thickness.10.mgh
*收件人：*"freesurfer","Ruopeng 
Wang"

*抄送：*

That command definitely will not work. When you ran the command I 
sent, did it at least show you something on the surface?


Ruopeng, is there a way to load a surface-based timecourse in freeview?

doug




On 2/26/14 9:11 PM, charujing123 wrote:

Hi doug,
Thanks doug.
I am sorry to describe my question no very clearly.It did work,but I 
want to view time course of lh.score.thickness.00.mgh vertex by 
vertex. So I need to try -v option to view time course manually as 
you just told me. However I cannot view anything but darkness when I 
try ""freeview -v lh.score.thickness.00.mgh"". Is there any tool or 
method to present a time course window(or a colume of numbers) when I 
click one voxel or vertex. And numbers in time course window will 
change when I click other voxel or vertex.

Thanks,
All the best.
Rujing Zha
2014-02-27

charujing123

*发件人：*Douglas N Greve 
*发送时间：*2014-02-27 01:51
*主题：*Re: [Freesurfer] time course in mri_info 
lh.gender_age.thickness.10.mgh

*收件人：*"freesurfer"
*抄送：*
Try this
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh 


Don't use -v in this case because -v is for a volumes and volume
overlays and all your data are surface overlays
On 02/25/2014 08:38 PM, charujing123 wrote:
> Hi doug and others,
> It will be highly appreciated,if anyone can help me.
> Thanks.
> All the best.
> Rujing Zhas
> 2014-02-26
>  


> charujing123
>  


> *发件人：*"charujing123"
> *发送时间：*2014-02-25 12:01
> *主 题：*Re: [Freesurfer] time course in mri_info
> lh.gender_age.thickness.10.mgh
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 


> *抄送：*
> Hi doug,
> When I try to do this by "freeview -f
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh 


> -v lh.score.thickness.00.mgh" or "freeview -v
> lh.score.thickness.00.mgh", it did create a window of time course.
> However there is nothing in the freeview window except
> darkness((i.e.fig1 in the attachment)). By the way, I can see
> something by "freeview -f
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh"(i.e.fig2 


> in the attachment). All of these can be got in the attachment.
> Thanks.
> All the best.
> Rujing Zha
> 2014-02-25
>  


> charujing123
>  


> *发件人：*"charujing123"
> *发送时间：*2014-02-25 10:28
> *主 题：*Re: [Freesurfer] time course in mri_info
> lh.gender_age.thickness.10.mgh
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 


> *抄送：*
> Thanks doug
> All the best.
> Rujing Zha
> 2014-02-25
>  


> charujing123
>  


> *发件 人：*Douglas N Greve 
> *发送时间：*2014-02-25 00:31
> *主 题：*Re: [Freesurfer] time course in mri_info
> lh.gender_age.thickness.10.mgh
> *收件 人：*"freesurfer"
> *抄送：*
> On 02/23/2014 08:32 PM, charujing123 wrote:
> > Hi all,
> > I have two questions.
> > 1,If I want to get the value of specific voxel from the
> > lh.gender_age.thickness.10.mgh, which code can I use to perform it?
> You can go to that vertex when you have it loaded into FreeView,
> otherwise you can load it into matlab (MRIread.m). Make sure to account 


> for the fact that matlab uses 1-based indices whereas FS uses 0-based.
> > 2,How to graph the time course of specfic voxel from the
> > lh.gender_age.thickness.10.mgh by freeview?
> Add "-v lh.gender_age.thickness.10.mgh" to your freeview command line
>

Re: [Freesurfer] freeview bug

[Ruopeng Wang]

This actually happens on any random non-annotation file. I'll fix it.

Ruopeng

On 03/14/2014 08:25 AM, Bruce Fischl wrote:
> Hi Jeff
>
> if you send us the .csv file we will see if we can replicate and fix
>
> cheers
> Bruce
> On Thu,
> 13 Mar 2014, Jeff Stevenson wrote:
>
>> hi freesurfer folks, just had a nasty bug crash my whole mac workstation. 
>> yikes! i loaded lh and rh pial surfaces into freeview and went to assign
>> annotation files to each and when i did i inadvertantly (aka randomly) 
>> selected the wrong file in labels dir- a .csv file i believe - instead of 
>> throwing an error dialogue with an appropriately snarky message it brought 
>> my whole system down, protected memory and all. never seen that before. 
>> after automatic reboot all was fine but this one is nasty. all current work 
>> was lost. hw was std mac pro osx 10.7.5, 96 GB mem.
>>
>> jeff
>>
>>
>> ___
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>>
>>
>>
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Re: [Freesurfer] Freeview, fsaverage_sym & aparc.annot

[Ruopeng Wang]

It appears to have the same issue on Linux as well. Thanks for the feedback. We 
will look into it.

Ruopeng

On Apr 9, 2014, at 5:53 PM, Peggy Skelly  wrote:

> Hi Freesurfer experts,
> 
> I'm trying to view aparc.annot on a fsaverage_sym surface. 
> 
> I can load aparc.a2009a.annot with
> 
> freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.a2009s.annot 
> but attempting 
> 
> 
> freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.annot
> 
> results in  freeview crashing. The command window output is in the attached 
> text file.
> 
> (Freeview 1.0 May 14, 2013; Mac OS 10.9.2)
> 
> Thanks,
> 
> Peggy
> 
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Re: [Freesurfer] Installing only Freeview

[Ruopeng Wang]

I have a stand-alone FreeView build for Mac that doesn't even need 
license file to run. Can we distribute it?

Ruopeng

On 04/11/2014 10:53 AM, Bruce Fischl wrote:
> probably all you need is the freeview binary and the license file, but 
> Ruopeng can confirm
> Bruce
> On Fri, 11 Apr 2014, Janosch Linkersdörfer wrote:
>
>> Hi all,
>>
>> is there a way, to install only freeview not the whole Freesurfer 
>> package (on Mac OS X). Or, alternatively, can somebody please tell me 
>> what I can safely remove after installing the whole package to be 
>> able to still run Freeview, but save the maximum of hard disk space?
>>
>> I do all processing on a remote computing server, but my VNC 
>> connection does not allow to display freeview, so I use sshfs to 
>> mount the server locally on my MacBook and use the local Freeview to 
>> inspect or correct files.
>>
>> Thanks,
>>
>> Janosch
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>

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Re: [Freesurfer] Installing only Freeview

[Ruopeng Wang]

OK. I'll put in license checking.

On 04/11/2014 10:57 AM, Bruce Fischl wrote:
> I think we need to distribute it with a license for NIH-accounting 
> purposes. The license is free and trivial to get so it's not really 
> much of a hardship
> On Fri, 11 Apr 2014, Ruopeng Wang wrote:
>
>> I have a stand-alone FreeView build for Mac that doesn't even need 
>> license file to run. Can we distribute it?
>>
>> Ruopeng
>>
>> On 04/11/2014 10:53 AM, Bruce Fischl wrote:
>>> probably all you need is the freeview binary and the license file, 
>>> but Ruopeng can confirm
>>> Bruce
>>> On Fri, 11 Apr 2014, Janosch Linkersdörfer wrote:
>>>
>>>> Hi all,
>>>>
>>>> is there a way, to install only freeview not the whole Freesurfer 
>>>> package (on Mac OS X). Or, alternatively, can somebody please tell 
>>>> me what I can safely remove after installing the whole package to 
>>>> be able to still run Freeview, but save the maximum of hard disk 
>>>> space?
>>>>
>>>> I do all processing on a remote computing server, but my VNC 
>>>> connection does not allow to display freeview, so I use sshfs to 
>>>> mount the server locally on my MacBook and use the local Freeview 
>>>> to inspect or correct files.
>>>>
>>>> Thanks,
>>>>
>>>> Janosch
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>
>>
>>

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Re: [Freesurfer] freeview fails to open

[Ruopeng Wang]

Have you tried dev version?

On May 6, 2014, at 10:15 AM, "jaco...@nmr.mgh.harvard.edu" 
 wrote:

> Hello All,
> 
> Any idea why freeview fails to open? Below I have included the terminal
> output.
> 
> I have checked my quota and I have plenty of available memory. I also
> tried running the 2 options (-start_in_debugger  and
> -on_error_attach_debugger), but these were not recognized. I was next
> going to attempt to configure, but I fear I may do more damage if I start
> messing around with cmds that I do not understand.
> 
> Thank you for the assistance!
> 
> Jacob
> 
> 
> [purkinje:mri] (nmr-stable53-env) freeview
> [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
> purkinje.nmr.mgh.harvard.edu by jacobml Tue May  6 10:07:13 2014
> [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
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Re: [Freesurfer] freeview fails to open

[Ruopeng Wang]

Just run:
source /usr/local/freesurfer/nmr-dev-env 

> On May 6, 2014, at 10:34 AM, "jaco...@nmr.mgh.harvard.edu" 
>  wrote:
> 
> I have not tried dev version. Can you please let me know how I can load that?
> 
>> Have you tried dev version?
>> 
>> On May 6, 2014, at 10:15 AM, "jaco...@nmr.mgh.harvard.edu"
>>  wrote:
>> 
>>> Hello All,
>>> 
>>> Any idea why freeview fails to open? Below I have included the terminal
>>> output.
>>> 
>>> I have checked my quota and I have plenty of available memory. I also
>>> tried running the 2 options (-start_in_debugger  and
>>> -on_error_attach_debugger), but these were not recognized. I was next
>>> going to attempt to configure, but I fear I may do more damage if I
>>> start
>>> messing around with cmds that I do not understand.
>>> 
>>> Thank you for the assistance!
>>> 
>>> Jacob
>>> 
>>> 
>>> [purkinje:mri] (nmr-stable53-env) freeview
>>> [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
>>> purkinje.nmr.mgh.harvard.edu by jacobml Tue May  6 10:07:13 2014
>>> [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
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>> 
>> 
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Re: [Freesurfer] Lost toolbar in freeview

[Ruopeng Wang]

What system are your running it on? I found it strange "defaults 
domains" only shows one item.


On 10/05/2015 11:23 AM, Antonin Skoch wrote:

Dear Ruopeng,

I have the same problem with missing toolbars in freeView, however I 
am not successful with command


defaults delete edu.harvard.mgh.nmr.FreeView

The command shows:

defaults delete: couldn't remove non-existent domain 
edu.harvard.mgh.nmr.FreeView

My command

defaults domains

shows only NSGlobalDomain - There is no FreeView defaults domain.

I am using freeView version 1.0.

Regards,

Antonin Skoch


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Re: [Freesurfer] Lost toolbar in freeview

[Ruopeng Wang]

Can you also try

delete ~/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plist

Try that and "defaults delete..." together.

On 10/05/2015 12:16 PM, Ruopeng Wang wrote:
What system are your running it on? I found it strange "defaults 
domains" only shows one item.


On 10/05/2015 11:23 AM, Antonin Skoch wrote:

Dear Ruopeng,

I have the same problem with missing toolbars in freeView, however I 
am not successful with command


defaults delete edu.harvard.mgh.nmr.FreeView

The command shows:

defaults delete: couldn't remove non-existent domain 
edu.harvard.mgh.nmr.FreeView

My command

defaults domains

shows only NSGlobalDomain - There is no FreeView defaults domain.

I am using freeView version 1.0.

Regards,

Antonin Skoch


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Re: [Freesurfer] Lost toolbar in freeview

[Ruopeng Wang]

In that case, simply click right-mouse button on the empty space on the menu 
bar. There should be a tiny menu item says “tool bar”. Check it and you should 
see tool bar again.

Best,
Ruopeng

> On Oct 6, 2015, at 6:32 AM, Antonin Skoch  wrote:
> 
> Dear Ruopeng,
> 
> I am using Ubuntu 12.04. LTS 32bits.
> 
> There is no directory
> ~/Library/Preferences
> 
> in my home directory. There is only "GNUstep" directory containing 
> subdirectories "Defaults" and "Library". "Library" dir is empty and 
> "Defaults" contains .GNUstepDefaults file, which is very short file 
> containing only NSGlobalDomain entry.
> 
> Regards,
> 
> Antonin
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Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Ruopeng Wang]

There was a bug in freeview in FS 5.3.0 that may have caused the crash. 
Clara, can you try the dev version of freeview?


Ruopeng

On 11/03/2015 11:50 AM, Bruce Fischl wrote:

Hi Clara

that doesn't crash for me. Are you sure you ahve write permission to 
the file? And that the disk isn't full? Ruopeng: any other ideas?


Bruce

On Tue, 3 Nov 2015, Clara Kühn wrote:


Hi Bruce,

I attached the wm.mgz from one of my participants. It happens with 
any participant though.
What I did is add wm voxels ( 147, 106, 68 ) and klick the save 
button and then it crashes with afore mentioned error message.


Cheers, Clara

- Ursprüngliche Mail -
Von: "Bruce Fischl" 
An: "Freesurfer support list" 
Gesendet: Dienstag, 3. November 2015 14:42:25
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Hi Clara

can you send us the wm.mgz and tell us exactly what you did to make it
crash?

thahks
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:


Dear FreeSurfer experts,

since last week I have the problem that FS (5.3.0) crashes when I 
try to save changes to the wm.mgz. It closes immediately and the 
wm.mgz is deleted. I can always restore it by renaming the temporary 
file (wm.mgz~) but it obviously doen't save any changes.


I've tried different computers (same FS version) and on some it 
works and on some the same problem occurs. I just tried it on the 
6.0.0beta version and it saved like a charm. I would rather, 
however, keep editing my data with the same version.

Here is the error message I get in the terminal:

[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 etsch by ckuehn 
Fri Oct 30 17:22:55 2015
[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)

Any idea what it means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn

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Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Ruopeng Wang]

Try 6.0.0beta.

On 11/03/2015 12:02 PM, Clara Kühn wrote:
> Our IT guy said it could be a software problem since he didn't have the 
> problem and the only difference between out computers was the display.
> We have these versions at the institute:
>
> 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta
> Is the first one the dev version?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Ruopeng Wang" 
> An: "Freesurfer support list" 
> Gesendet: Dienstag, 3. November 2015 17:57:50
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> There was a bug in freeview in FS 5.3.0 that may have caused the crash. 
> Clara, can you try the dev version of freeview?
>
> Ruopeng
>
> On 11/03/2015 11:50 AM, Bruce Fischl wrote:
>
>
> Hi Clara
>
> that doesn't crash for me. Are you sure you ahve write permission to the 
> file? And that the disk isn't full? Ruopeng: any other ideas?
>
> Bruce
>
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Hi Bruce,
>
> I attached the wm.mgz from one of my participants. It happens with any 
> participant though.
> What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and 
> then it crashes with afore mentioned error message.
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Bruce Fischl" 
> An: "Freesurfer support list" 
> Gesendet: Dienstag, 3. November 2015 14:42:25
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> Hi Clara
>
> can you send us the wm.mgz and tell us exactly what you did to make it
> crash?
>
> thahks
> Bruce
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Dear FreeSurfer experts,
>
> since last week I have the problem that FS (5.3.0) crashes when I try to save 
> changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
> always restore it by renaming the temporary file (wm.mgz~) but it obviously 
> doen't save any changes.
>
> I've tried different computers (same FS version) and on some it works and on 
> some the same problem occurs. I just tried it on the 6.0.0beta version and it 
> saved like a charm. I would rather, however, keep editing my data with the 
> same version.
> Here is the error message I get in the terminal:
>
> [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 etsch by ckuehn Fri Oct 30 
> 17:22:55 2015
> [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)
>
> Any idea what it means by Segmentation Violation and how I can fix it??
> Cheers and thanks in advance!
> Clara Kühn
>
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Re: [Freesurfer] How to compute area of subcortical structures

[Ruopeng Wang]

Hi Anirudh,

Lee was right. Label stats shown in freeview is for volume labels. It shows the 
stats of the underlying volume slice in that label.  It should not be compared 
with surface area.

Best,
Ruopeng

> On Nov 11, 2015, at 5:57 AM, anirudh nihalani  
> wrote:
> 
> Hi Bruce,
> 
>Sorry I forgot to attach the files mentioned in my last email. PFA the 
> files here. Thank you.
> 
> Regards,
> Anirudh
> 
> On Wed, 11 Nov 2015 at 16:18 anirudh nihalani  > wrote:
> Hi Bruce,
> 
> Thank you very much for your quick reply. Sorry I hadn't been able to 
> reply faster as I was trying to figure out the below mentioned issue from two 
> days.
> 
>  I have computed surface area of left-hippocampus using the commands 
> mri_tessellate and mris_info. However I found that in freeview by selecting 
> Tools->show label stats, I am able to display area of any label (PFA a 
> screenshot) but these area stats do not match with the areas obtained using 
> mri_tessellate and mris_info. I have two queries regarding this:
> 
> 1) Surface areas of labels displayed in freeview doesn't match with 
> subcortical structures' areas obtained by running mri_tesselate and 
> mris_info. For example the attached screenshot shows that area of 
> left-hippocampus is 71 mm^2 where as mri_tessellate followed by mris_info 
> found the area for left-hippocampus to be 3586 (PFA the output of 
> mris_tessellate and mris_info). Why is there a mismatch?
> 
> 2) Based on your reply I thought area stats are not calculated for 
> subcortical structures during "recon-all". If that is the case, how is 
> freeview displaying area stats for subcortical areas? Also which file does 
> freeview use to display these stats? Is it stats/[l/r]h.aparc.stats? I ask 
> because even cortical structures' areas displayed by freeview are not 
> matching with what is stored in these files.
> 
> Please let me know. Thank you.
> 
> Regards,
> Anirudh
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Re: [Freesurfer] Trackvis/ Diffusion Toolkit

[Ruopeng Wang]

Hi Alan,

The tracks look weird. Why are they so straight?

Ruopeng

> On Nov 12, 2015, at 2:14 PM, Alan Francis  wrote:
> 
> Hi Anastasia:
> 
> It was great to meet you at the connectivity course at Martinos. I have been 
> using Trackvis to examine the white matter tracks between the anterior insula 
> and the Dorsal ACC. In line with your instruction, I created ROIS at each of 
> these regions. However, the WM tracks generated do not appear to connect. I 
> have attached a screenshot.
> 
> What is the command that one would use to connect the ROIs? 
> 
> thanks so much,
> 
> best regards,
> 
> Alan
> 
> -- 
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> 
> Alan N. Francis PhD
> NIDA T32  Fellow in Computational Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu  
> afran...@mclean.harvard.edu 
>   
>  
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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Re: [Freesurfer] Trackvis/ Diffusion Toolkit

[Ruopeng Wang]

In your log:

"- Launching hardi_mat -


Number of measurement points: 6
"


6 directions will not be enough for a hardi/Qball reconstruction. There 
is something wrong with your selected gradient table. Which did you choose?




On 11/13/2015 10:16 AM, Alan Francis wrote:

Hi Ruopeng:

These brains have been run on Tracula and they look good. As a post 
processing step, I wanted to look at the connectivity between the DACC 
and anterior insula using DTK and Trackvis. Here is what I did:


- Launching hardi_mat -


Number of measurement points: 6

1. I used the Imaging model HARDI/Q-Ball since these were acquired 
using the HARDI method.


2. I clicked the 'reconstruction' button.

3.  Next I loaded the dwi.nii.gz

I clicked on the load TrackVIS option.

I did not fill in any other option.

It ran without problems. Here is the script:

 11/12/15 1:14 PM 


Steps to do:


1. hardi_mat 
"/var/folders/97/_lbh5hkn2b57h_hvks9m2bp8gq/T/dtk_tmp/matrices/gradient.txt" 
"/var/folders/97/_lbh5hkn2b57h_hvks9m2bp8gq/T/dtk_tmp/matrices/temp_mat.dat" 
-ref "/Users/afrancis/Desktop/Connectome/101309/dmri/dwi.nii.gz" -oc



2. odf_recon 
"/Users/afrancis/Desktop/Connectome/101309/dmri/dwi.nii.gz" 7 181 
"/Users/afrancis/Desktop/Connectome/101309/dmri/hardi" -b0 1 -mat 
"/var/folders/97/_lbh5hkn2b57h_hvks9m2bp8gq/T/dtk_tmp/matrices/temp_mat.dat" 
-p 3 -sn 1 -ot nii



3. odf_tracker "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi" 
"/var/folders/97/_lbh5hkn2b57h_hvks9m2bp8gq/T/dtk_tmp/track_tmp.trk" 
-at 35 -m 
"/Users/afrancis/Desktop/Connectome/101309/dmri/hardi_dwi.nii" -it nii



4. spline_filter 
"/var/folders/97/_lbh5hkn2b57h_hvks9m2bp8gq/T/dtk_tmp/track_tmp.trk" 
1 "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi.trk"



5. trackvis "/Users/afrancis/Desktop/Connectome/101309/dmri/hardi.trk"


- Launching hardi_mat -


Number of measurement points: 6

Number of reconstruction points: 181


- Launching odf_recon -


Volume dimension: 145 174 145

Voxel size: 1.250 1.250 1.250

Reading recon matrix...

done

Matrix file being used: 
/var/folders/97/_lbh5hkn2b57h_hvks9m2bp8gq/T/dtk_tmp/matrices/temp_mat.dat




Reconstructing data... 100%


Writing b0 map...Done.

Writing dwi map...Done.

Reconstruction completed successfully.

Time taken: 00:04:43


- Launching odf_tracker -


Volume dimension: 145 174 145

Voxel size: 1.250 1.250 1.250


Threshold for mask one: 92.9688 2945



Reading odf max data... 100%

Tracking... 100%


Time taken: 00:05:40


- Launching spline_filter -


Volume dimension: 145 174 145

Voxel size: 1.25 1.25 1.25


Spline filtering track data...Done.

Number of tracks: 4586640


- Launching trackvis -


TrackVis successfully launched.


Total time taken: 00:15:32



However, when I looked at the generated tracks, they looked weirdly 
straight.  I have a hunch that I am processing 'already processed' 
brains and hence this anomaly.



Please advice.


Thanks,


Alan

- Launching hardi_mat -


Number of measurement points: 6


On Thu, Nov 12, 2015 at 4:20 PM, Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>> wrote:


Hi Alan,

The tracks look weird. Why are they so straight?

Ruopeng


On Nov 12, 2015, at 2:14 PM, Alan Francis
mailto:alandarkene...@gmail.com>> wrote:

Hi Anastasia:

It was great to meet you at the connectivity course at Martinos.
I have been using Trackvis to examine the white matter tracks
between the anterior insula and the Dorsal ACC. In line with your
instruction

- Launching hardi_mat -


Number of measurement points: 6

, I created ROIS at each of these regions. However, the WM tracks
generated do not appear to connect. I have attached a screenshot.

What is the command that one would use to connect the ROIs?

thanks so much,

best regards,

Alan

-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*
Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu <mailto:ezra_wegbr...@brown.edu>
afran...@mclean.harvard.edu <mailto:afran...@mclean.harvard.edu>

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Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs

[Ruopeng Wang]

Hi David,

Freeview can’t load flat patches now. We will add it to the list of pending 
features for the future update.

Best,
Ruopeng

> On Dec 12, 2015, at 11:07 AM, Slater David  wrote:
> 
> I use freeview a lot and have never had any problems with it. However I want 
> to work on occipital patches to do retinotopy.
> 
> Can freeview load flat patches? Is there a way to display complex data 
> overlays to produce phase maps as was possible in tksurfer?
> 
> Thanks,
> David
> 
> 
> -Message d'origine-
> De : freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce Fischl
> Envoyé : 12 December 2015 16:45
> À : Freesurfer support list
> Objet : Re: [Freesurfer] configure overlay display in tksurfer by keyboard 
> inputs
> 
> Hi David
> 
> tksurfer has been deprecated - can you try using freeview instead?
> Bruce
> On Sat,
> 12 Dec 2015, Slater David wrote:
> 
>> Hi,
>> 
>> I have the same problem with tksurfer in Ubuntu.
>> 
>> The keyboard entry doesn't work for the tksurfer input boxes - I can't set 
>> any values in the overlay configuration window, edit label info, configure 
>> phase encoded data display etc. All of the text / numeric entry boxes have 
>> this issue.
>> 
>> Any suggestions on how to fix this?
>> 
>> My freesurfer verion is 
>> freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 but I had the same 
>> problem before updating to v6-beta.
>> 
>> Thanks,
>> David
>> 
>> 
>> -Message d'origine-
>> De : freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce 
>> Fischl Envoyé : 15 August 2015 21:12 À : Freesurfer support list Objet 
>> : Re: [Freesurfer] configure overlay display in tksurfer by keyboard 
>> inputs
>> 
>> Hi Lars
>> 
>> can you give more details? What prevents you from entering values? Do you 
>> get any errors when tksurfer loads?
>> 
>> cheers
>> Bruce
>> 
>> On Sat,
>> 15 Aug 2015, Lars M. Rimol wrote:
>> 
>>> 
>>> Hi all,
>>> 
>>> I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am 
>>> unable to set threshold values in the edit boxes in the "configure 
>>> overlay" display in tksurfer. Does anybody know how to fix this (without 
>>> specifying the threshold on the command line each time)?
>>> 
>>> Thank you!
>>> 
>>> 
>>> 
>>> 
>>> 
>>> yours,
>>> Lars M. Rimol, PhD
>>> Department of Medicine
>>> John A. Burns School of Medicine
>>> University of Hawai'i
>>> 1356 Lusitana Street, University Tower Honolulu, HI 96813
>>> 
>>> 
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Re: [Freesurfer] freeview automatization not working nicely

[Ruopeng Wang]

Hi Max,

Please try putting each command as a separate line, like this:

-v scan1/mri/T1.mgz
-v scan1/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2
etc..

Best,
Ruopeng



> On Dec 17, 2015, at 5:30 AM, BAUTISTA-PERPINYA Maximilià 
>  wrote:
> 
> Hi FS experts, 
> 
> I have an script (screenshots.txt) that takes screenshots of freeview of 
> several scans:
> 
> It looks like this:
> 
> -v scan1/mri/T1.mgz ; -v scan1/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; 
> -viewport sagittal -slice 80 127 127 -ss sag1_scan1  ; -v scan2/mri/T1.mgz ; 
> -v scan2/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; -viewport sagittal 
> -slice 80 127 127 -ss sag1_scan2  ; ... and so on
> 
> Then I run freeview -cmd screenshots.txt and it gives me this error: 
> MRIread failed: Unable to read from 
> /home/freesurfer/Desktop/test005/subjects/;
> 
> 
> This path is my cwd. The scan folders (scan1, scan2, and so on) are contained 
> within the above mentioned cwd, but the cwd is not mentioned in the script. I 
> tried specifying the complete path 
> (/home/freesurfer/Desktop/test005/subjects/scan1 and so on) but gives the 
> same error. 
> 
> As well, the only output from this is the screenshot from the last scan 
> (sag1_scan2 in this case). The other ones before are missing. 
> 
> Anybody knows a way around this? Any help would be much appreciated 
> 
> Best regards, 
> 
> 
> Max Bautista
> 
> 
> btw:
> -
> 
> FREESURFER_HOME: /usr/local/freesurfer
> 
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> 
> RedHat release: CentOS release 6.7 (Final)
> 
> Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
> 
> -
> 
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Re: [Freesurfer] Fwd: 3D viewing ROIs by Freeview

[Ruopeng Wang]

Hi Faezeh,

What do you mean by 3D brain map? Is it a 3D surface? What is the format 
of the ROIs you are trying to load?


Ruopeng

On 02/09/2016 02:01 PM, Faeze Vedaei wrote:

Hello Freesurfer experts,

I am Faezeh Vedaei a research assistant in a neurology lab at the 
Michigan State University. In my project I want to have a 3D view of 
ROIs which I just extracted by AFNI, after I executed recon-all. I 
would like to help me how can I overlay some specific ROIs on a 3D 
brain map in Freeview? In advance, I would appreciate your time and 
consideration.


Regards,
Faezeh Vedaei



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Re: [Freesurfer] TrackVis "either end" command

[Ruopeng Wang]

Hi Catherine,

This question might not fit in freesurfer mailing list but I'll answer here 
anyway - Unfortunately, for the command-line track_vis, there is no such 
option. 

Ruopeng

On May 7, 2013, at 9:53 AM, "Chu, Catherine,M.D."  wrote:

> Dear Freesurfer/TrackVis experts,
> 
> I am using the following command in a batchfile to identify tracks counts 
> between dozens of preset ROIs. 
> 
> track_vis DATAPATHtob0.trk -roi DATAPATHTOROI1.nii -roi2 DATAPATHTOROI2.nii 
> -o PATHTOOUTPUT.trk > OUTPUT.txt -nr', i, j, i, j, i, j
> 
> Is there a line command I can use so that the tracks identified follow the 
> rule "either end" in the ROIs instead of the default "any part"?
> 
> Thank you!
> Cat
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Re: [Freesurfer] Freeview automation

[Ruopeng Wang]

There is a screenshot option -ss from the command-line. Run 'freeview -h' will 
show you all the available options. 

Ruopeng

On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga  
wrote:

> Hi list, 
> is it possible to automate Freeview automation from the command line? 
> 
> I want to automatically render 3D images of the hippocampus (I have a 
> separate volume, based on hippo-subfields) and have an image for all subjects 
> for quality checking.
> 
> thanks!
> Gari 
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Re: [Freesurfer] Freeview automation

[Ruopeng Wang]

If you use '-ss' option, freeview will save a screenshot and close 
itself. For example:


freeview -v foo.mgz -ss foo.jpg

On 05/31/2013 11:13 AM, Ender Konukoglu wrote:

Sure.

I couldn't find that option neither.

What I did was to semi-automatize.
I wrote a batch file to call freeview multiple times with different 
parameters.
Each time freeview pops up and I save the image/video. During this 
time the process in the terminal waits for me.
When I shut that window the next freeview window pops up and I do the 
same.


Ender


On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:

Thanks!

I can visualize the 3D renders of interest with different colors, but 
from "freeview -h" I couldn't get the following: is it possible to 
automatize the "File > Save movie frames" option?


Thanks again!
Gari



On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias 
mailto:igles...@nmr.mgh.harvard.edu>> 
wrote:


Ender asked me to forward you this:

I had to automate freeview recently.
Freeview can be used via command line.
For options please write
freeview -h
in the console / terminal.

An example command that produces a surface and overlays a map on it:
freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180

Let me know if this helps.

Cheers,

E




    On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
> There is a screenshot option -ss from the command-line. Run
'freeview -h' will show you all the available options.
>
> Ruopeng
>
> On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga
mailto:gariko...@gmail.com>> wrote:
>
> > Hi list,
> > is it possible to automate Freeview automation from the
command line?
> >
> > I want to automatically render 3D images of the hippocampus
(I have a separate volume, based on hippo-subfields) and have an
image for all subjects for quality checking.
> >
> > thanks!
> > Gari
> > ___
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
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>
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>

--
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu <mailto:igles...@nmr.mgh.harvard.edu>
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.





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Re: [Freesurfer] is it a bug of freeview? or wrong segmentation?

[Ruopeng Wang]

Can you try re-run that freeview command again? I remember I saw similar 
problem once, but somehow I could not reproduce it when I re-run the 
same command. If you can positively reproduce it, would it be possible 
to send us all the files that are used in the command?


Best,
Ruopeng

On 6/26/12 3:41 AM, Chao Suo wrote:


Hi all,

I am new with freesurfer, and I found a problem when processing some 
data following the instruction online.


When I checked the surfaces of these two timepoint together using 
freeview (follow the instruction online), it showed this abnormal 
spike on the white mater surface of my time point two scan. (fig 1, 
left, clear version: https://dl.dropbox.com/u/4825915/fig1.png)


freeview -v SMART001aT1.long.SMART001T1/mri/norm.mgz \

SMART001bT1.long.SMART001T1/mri/norm.mgz \

-f SMART001aT1.long.SMART001T1/surf/lh.pial:edgecolor=red \

   SMART001aT1.long.SMART001T1/surf/lh.white:edgecolor=blue \

SMART001bT1.long.SMART001T1/surf/lh.pial:edgecolor=255,128,128 \

SMART001bT1.long.SMART001T1/surf/lh.white:edgecolor=lightblue \

However, it was wired that I couldn't see this spike when I opened 
them in tkmedit. (fig1, right, https://dl.dropbox.com/u/4825915/fig1.png)


tkmedit SMART001bT1.long.SMART001T1 brainmask.mgz -aux wm.mgz --surfs

Further, if I inspected only the two surfaces of my time two data, 
there is no such spike at the same point. (fig2, clear version: 
https://dl.dropbox.com/u/4825915/fig2.png)


freeview -v SMART001bT1.long.SMART001T1/mri/norm.mgz \

-f SMART001bT1.long.SMART001T1/surf/lh.pial:edgecolor=255,128,128 \

SMART001bT1.long.SMART001T1/surf/lh.white:edgecolor=lightblue \

So I am not sure whether these spikes are bugs when using freeview, or 
actually some registration error that need me to edit. Can some help 
me to confirm it? Or, did anyone come across this problem before?


Thanks

Chao Suo



PhD Candidate, School of Psychiatry, UNSW, Australia

Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY

Room 401, Level 4, M02K | 100 Mallett St Camperdown | NSW | 2050

T +61 2 9351 0728  | F +61 2 9351 0551 |



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Re: [Freesurfer] Freeview scripting reference

[Ruopeng Wang]

Hi Inge,

Freeview does not support tcl scripting. It does have lots of 
command-line options that might fit your need. Run 'freeview -h" will 
display a complete list of the available options.


Best,
Ruopeng

On 6/29/12 7:16 AM, Inge Kasbohm Amlien wrote:

Hi list,
I am looking for a complete reference to scriptable commands for 
Freeview, comparable to what exists for tksurfer (e.g. 
http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference)


Does this exist?

Thanks!

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Phone: +47 97106525
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Centre for the Study of Human Cognition
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Re: [Freesurfer] request for move through slices

[Ruopeng Wang]

Hi Michael,

In freeview you can press Page up/down keys to move through slices.

Best,
Ruopeng

On 7/2/12 5:30 AM, Michael Scheel wrote:
> Dear FS experts,
>
> I am trying out freeview and am extremely fond of it.
> I have one feature request. In tkmedit in navigate mode it was possible 
> moving through slices just using the mouse (middle mouse button pressed).
> Is it possible to implement the same in freeview - it appears that in 
> freeview there are two zoom mouse actions scroll wheel
> and pressing-middle-mouse-button while moving up and down. Having this 
> feature would ease checking and correcting data a lot.
>
> Thanks, Michael
>
>
>
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Re: [Freesurfer] freeview

[Ruopeng Wang]

Hi, Freeview does not look up SUBJECT environment variable. So you will 
need to cd into your subject directory before running the command, or 
use the full path in the command for every file.


Ruopeng

On 11/7/12 9:50 AM, Catherine Bois wrote:
Hi, I am trying to use freeview to look at wm/brainmask etc however 
the command wont work. The command Im suing is

freeview -v wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4 
wm1_edits_before/mri/brainmask.mgz \
-f wm1_edits_before/surf/lh.white:edgecolor=blue 
wm1_edits_before/surf/lh.pial:edgecolor=red \
wm1_edits_before/surf/rh.white:edgecolor=blue 
wm1_edits_before/surf/rh.pial:edgecolor=red

(but i am exchanging paths for my own data). However, it keeps saying that 
operation console failed, and for some reason, even though Ive set the subject 
directory to where the files are kept it

keeps looking in my home directory. I recently attended a course in freesurfer, 
but this problem was not explained? Grateful for help.


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Re: [Freesurfer] freeview warning: invalid drawable

[Ruopeng Wang]

On a Mac? You can just ignore those warning messages. Unfortunately we 
were unable to remove them.


Ruopeng

On 03/20/2013 04:07 PM, Glen Lee wrote:

Dear freesurfer experts,
I'm wondering why I get this warning message when I open up any surf 
template in either fsaverage or fsaverage_sym directory.

FYI, I'm using freeview v1.0
if anybody know, please help.
-Glen

$ freeview -f lh.inflated
2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.805 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.823 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.825 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.844 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.846 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.863 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.865 freeview.bin[52449:907] invalid drawable
QObject::connect: Connecting from QAbstractButton::toggled(bool) to 
COMPAT slot (QGroupBox::setShown(bool))
QObject::connect: Connecting from QAbstractButton::toggled(bool) to 
COMPAT slot (QGroupBox::setShown(bool))

2013-03-20 16:03:06.211 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:06.212 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:06.213 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.634 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.638 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.649 freeview.bin[52449:907] invalid drawable



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Re: [Freesurfer] More freeview feature requests

[Ruopeng Wang]

Hi Chris,

Thanks for the suggestions. We’ll put them in future update.

Best,
Ruopeng

> On Jan 25, 2017, at 2:54 AM, Chris Adamson  wrote:
> 
> Freesurfer devs,
>  
> Freeview is really nice to use. I have a few more suggestions:
>  
> It would be good to have keyboard shortcuts to change the brush size ala. 
> Tkmedit.
> A clone feature ala tkmedit that would be needed to fill in brainmask or 
> brain.finalsurfs.manedit.mgz
> When you are saving control points you have to manually change to the tmp 
> directory and save as control.dat. It would be good to have an option that 
> would automatically create this file.
>  
> Thanks in advance,
>  
> Chris Adamson. 
> 
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Re: [Freesurfer] Freeview in 6.0 - editing labels

[Ruopeng Wang]

Hi Trisanna,

There is no straight-forward way to let you edit surface labels but you can try 
these steps:

1. Load a volume and a surface.
2. Load the label you want to edit as volume label (ROI).
3. Select the ROI in the layer list to bring up ROI property panel. Click on 
“Map to Surface” dropdown box and select the surface. You should see the label 
shown on the surface.
4. Switch to ROI Edit mode. You can start to edit the label on the surface. 
Click left mouse button to add vertex. Shift+Left button to remove vertex.
5. After edit, you might notice direct save button is still grayed out, which 
is a bug. But you can save it by “Save ROI as”. Sorry for the inconveneince.

In future update we plan to simply label editing by combining surface and 
volume labels. Hopefully that will make label editing a lot easier.

Best,
Ruopeng

> On Jan 25, 2017, at 11:48 AM, Trisanna Sprung-Much 
>  wrote:
> 
> 
> Hi there
> 
> Does the 6.0 version of Freeview have a way to edit labels on surfaces 
> similar to how tksurfer allowed us to do this?
> 
> Thanks!
> 
> Trisanna
> 
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
> 
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Re: [Freesurfer] Freeview v6.0 Draw ROI Bug - Only Brush Size of 1 Saved?

[Ruopeng Wang]

Hi Doug,

We will investigate and fix it asap.

Best,
Ruopeng 

> On Jan 25, 2017, at 4:13 PM, Douglas Merkitch  
> wrote:
> 
> Hello,
> 
> I think I have encountered a bug in freeview on 
> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. When I attempt to draw and 
> save an ROI label, I get the following error in the terminal:
> 
> QFileInfo::absolutePath: Constructed with empty filename
> 
> The ROI label does save, but when I open it, it's as if only the voxels that 
> my cursor had touched during the drawing process are saved and those that 
> were added by any brush size greater than 1 are not saved (see attached 
> screenshots). Also, the fill all "paint bucket" seems to work and save 
> correctly. When I revert to freeview v5.3 
> (freesurfer-Darwin-lion-stable-pub-v5.3.0) the ROI draw and save function 
> works without issue. 
> 
> Thanks,
> 
> Doug
> 
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Email: douglas_merki...@rush.edu
> 
> 
> 
> 
>  PM.png>
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Re: [Freesurfer] freeview command line options

[Ruopeng Wang]

Hi Peng,

No, there is no command-line option for that. I will add it in future update.

Best,
Ruopeng

> On Jan 27, 2017, at 9:49 AM, peng  wrote:
> 
> Dear Freesurfer experts,
> 
> When I use Freeview GUI to show overlays on a surface, I can click on
> the button "Configure", and then check the box "Enable" in the smooth
> section (upper right of the pop-out window), to smooth it. Is there
> any options to do similar stuff in the command line of freeview? e.g.
> when I want to generate a lot of screenshots by the -ss option.
> Thank you in advance!
> 
> best
> Peng
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Re: [Freesurfer] FS 6.0 Freeview

[Ruopeng Wang]

Or would it be possible to send us the full crash report?

> On Feb 17, 2017, at 10:17 AM, Z K  wrote:
> 
> Hi Dan. Is there an error output to the screen or terminal window? We 
> will probably need that to help diagnose the issue.
> 
> 
> 
> On 02/17/2017 05:31 AM, Daniel Carey wrote:
>> Dear All,
>> 
>> I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable
>> to load volumes in Freeview. When selecting 'File > Load volume', the
>> dialog box appears, but when I select any T1.mgz and click Ok, Freeview
>> immediately crashes.
>> 
>> Has anyone encountered this same issue?
>> 
>> Best wishes,
>> 
>> Dan
>> 
>> ---
>> Dr. Daniel Carey
>> Post-Doctoral Research Fellow - Statistician
>> The Irish LongituDinal Study on Ageing (TILDA)
>> Trinity College Dublin
>> Dublin 2, Ireland.
>> Email: care...@tcd.ie  > >
>> 
>> 
>> 
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Re: [Freesurfer] Freeview

[Ruopeng Wang]

Hi Nazanin,

To change color you will need to modify the look up table, i.e., load your own 
look up table. There is no way to only display a few selected labels. As a 
workaround, you may try applying a look up table with only a few labels in it. 

Best,
Ruopeng

> On Feb 21, 2017, at 5:20 AM, N Saf  wrote:
> 
> Dear Experts,
> 
> I load the T1 and aseg file in freeveiw and select the lookup table ,and show 
> as isosurface in 3D view for a label .Is it possible to change the color(for 
> example label 13 is blue but I want to show it as yellow!).another question 
> is that if I want to show multiple labels which are not in the range how 
> should I do it ? for example I want to see labels 11 & 13 & 30  but not the 
> lables between ,how can I do it?thanks for your support.
> 
> 
> Best Regards,
> Nazanin
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Re: [Freesurfer] Freeview

[Ruopeng Wang]

Just open FreeSurferColorLUT.txt file in your freesurfer installation 
directory, you should be able to figure the format. 

> On Feb 21, 2017, at 10:59 AM, N Saf  wrote:
> 
> Dear Ruopeng,
> 
> Thank you for the fast response ,where can I learn how to create my custom 
> lookup table step by step ? and what the format of this file is?any help will 
> be very appreciated.
> 
> Best Regards,
> Nazanin
> 
> On Tue, Feb 21, 2017 at 6:45 PM, Ruopeng Wang  <mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
> Hi Nazanin,
> 
> To change color you will need to modify the look up table, i.e., load your 
> own look up table. There is no way to only display a few selected labels. As 
> a workaround, you may try applying a look up table with only a few labels in 
> it.
> 
> Best,
> Ruopeng
> 
> > On Feb 21, 2017, at 5:20 AM, N Saf  > <mailto:nali...@gmail.com>> wrote:
> >
> > Dear Experts,
> >
> > I load the T1 and aseg file in freeveiw and select the lookup table ,and 
> > show as isosurface in 3D view for a label .Is it possible to change the 
> > color(for example label 13 is blue but I want to show it as 
> > yellow!).another question is that if I want to show multiple labels which 
> > are not in the range how should I do it ? for example I want to see labels 
> > 11 & 13 & 30  but not the lables between ,how can I do it?thanks for your 
> > support.
> >
> >
> > Best Regards,
> > Nazanin
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