Ugh -- you're not getting any breaks, are you?
caret5 has some options at launch:
-style style-name
Set the user-interface style where "style-name" is one of:
Windows
Motif
CDE
Plastique
GTK+
Cleanlooks
See if entering "caret5 -style Cleanlooks" works better.
On Dec 3, 2013, at 1:36 PM, Taosheng Liu <[email protected]> wrote:
> Hi Donna,
> The older version of caret_command works fine, in both preborder and
> postborder, but when we need to adjust the landmarks using caret5's GUI, we
> got this error:
>
> Gtk-CRITICAL **: IA__gtk_widget_style_get: assertion `GTK_IS_WIDGET (widget)'
> failed
>
> The computer then pretty much freezes. It seems there's something wrong with
> X-windows? We're running 64bit Linux (Ubuntu). Do you have any suggestions? I
> couldn't find any obvious solution by searching the web. The new caret5 GUI
> works just fine.
> Thank you,
>
> --ts
>
>
> On 11/27/2013 05:18 PM, Donna Dierker wrote:
>> Good question. You could use different versions for the two steps, but
>> you'd have to report that in your methods, which could get messy. Running
>> pre border.sh with the older caret_command probably wouldn't take that long,
>> but if you tweaked your borders, it could overwrite them, depending on what
>> you used for the borderproj update string (e.g., updated).
>>
>> To get around that, you could tar/zip just your tweaked borderproj files;
>> re-run preborder.sh; unzip the preserved tweaked borderproj; and run post
>> border.sh.
>>
>>
>> On Nov 27, 2013, at 2:01 PM, Taosheng Liu <[email protected]> wrote:
>>
>>> Thanks for the tip. Just another question, if we switch to the older
>>> version, do you think we should re-run the preborder script as well? or we
>>> can pick up from where preborder has ended and just run postborder with the
>>> older caret_command?
>>> Thank you,
>>>
>>> --ts
>>>
>>> On 11/27/2013 02:33 PM, Donna Dierker wrote:
>>>> I agree, the check_reg captures look great to me. The 144 cycles are
>>>> troubling. In your shoes, I'd revert.
>>>>
>>>>
>>>> On Nov 27, 2013, at 10:41 AM, Taosheng Liu <[email protected]> wrote:
>>>>
>>>>> Hi Donna,
>>>>> Thanks for testing this, and for your fast response. Yes we're not
>>>>> getting a core dump and it does finish, although with 144 cycles. Are you
>>>>> saying we should switch back to the old caret for the time being? I mean,
>>>>> the check_reg result seems fine, but maybe there's still something wrong
>>>>> with it?
>>>>> Thank you!
>>>>>
>>>>> --ts
>>>>>
>>>>>
>>>>>
>>>>> On 11/27/2013 11:27 AM, Donna Dierker wrote:
>>>>>> Hi Taosheng,
>>>>>>
>>>>>> I tried running postborder.sh on a dataset I have here, and I got a core
>>>>>> dump on the offending line:
>>>>>>
>>>>>> + caret_command -surface-sphere-multi-morph Human.SAIS_018.L.73730.spec
>>>>>> deformed_Human.SAIS_018.L.Midthickness_711-2B.mws.coord
>>>>>> Human.SAIS_018.L.SPHERICAL.73730.MWS.coord
>>>>>> Human.SAIS_018.L.CLOSED.73730.topo
>>>>>> ./PALS_B12.LR/postborder.sh: line 50: 27257 Segmentation fault
>>>>>> (core dumped) caret_command -surface-sphere-multi-morph $SPEC
>>>>>> $FIDUCIAL_MWS $SPHERE_MWS $TOPO
>>>>>>
>>>>>> You're not getting a core dump, but something else is clearly going awry
>>>>>> with that line.
>>>>>>
>>>>>> I tried backtracking to a June 2011 vintage caret, and it completed with
>>>>>> no problems. Here is the version I used:
>>>>>>
>>>>>> http://brainvis.wustl.edu/pub/caret/caret_distribution_Linux64.v5.64.zip
>>>>>> login pub
>>>>>> password download
>>>>>>
>>>>>> Here are the logs for the for the two versions of caret (bad and good):
>>>>>>
>>>>>> Problem log:
>>>>>> http://brainmap.wustl.edu/pub/donna/US/MI/postborder.log
>>>>>> Good log:
>>>>>> http://brainvis.wustl.edu/pub/donna/US/MI/postborder.201106.log
>>>>>>
>>>>>> I'm not sure when caret_command will be fixed, but I will pass the
>>>>>> dataset and details on to the developers.
>>>>>>
>>>>>> Donna
>>>>>>
>>>>>>
>>>>>> On Nov 26, 2013, at 11:58 AM, Donna Dierker <[email protected]>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Taosheng,
>>>>>>>
>>>>>>> I am going to try postborder.sh on my new Linux box and see if it does
>>>>>>> the same thing.
>>>>>>>
>>>>>>> I don't see any candidate culprits in my ~/.caret5_preferences file.
>>>>>>>
>>>>>>> No one else has reported this issue. More users are moving to the
>>>>>>> fs_LR pipeline:
>>>>>>>
>>>>>>> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs_LR
>>>>>>>
>>>>>>> There are trade-offs which are discussed here:
>>>>>>>
>>>>>>> http://cercor.oxfordjournals.org/content/early/2011/11/02/cercor.bhr291.full.pdf+html
>>>>>>>
>>>>>>> One big plus is that there is no border tweaking.
>>>>>>>
>>>>>>> I'll let you know how my post border.sh trial comes out, or if I need
>>>>>>> sample data. But I think I have plenty of sample data right here. I
>>>>>>> can't imagine what might be unique about our data that would cause this.
>>>>>>>
>>>>>>> Donna
>>>>>>>
>>>>>>>
>>>>>>> On Nov 26, 2013, at 8:22 AM, Taosheng Liu <[email protected]> wrote:
>>>>>>>
>>>>>>>> Hi Donna,
>>>>>>>> Yes I can see that line of code in the script. Have you other others
>>>>>>>> on this list run this command lately? I wonder if you also see this
>>>>>>>> many cycles. If not, I wonder if there is some global setting I should
>>>>>>>> set, or something is off with my data. I can certainly supply the data
>>>>>>>> if needed.
>>>>>>>> Thank you,
>>>>>>>>
>>>>>>>> --Taosheng
>>>>>>>>
>>>>>>>>
>>>>>>>> On 11/25/2013 06:50 PM, Donna Dierker wrote:
>>>>>>>>> Hmmm. Your results look great, but 144 cycles of spherical morphing
>>>>>>>>> is certainly not normal. I think the line in the script that does
>>>>>>>>> this is this one:
>>>>>>>>>
>>>>>>>>> #MULTIRESOLUTION MORPHING
>>>>>>>>> caret_command -surface-sphere-multi-morph $SPEC $FIDUCIAL_MWS
>>>>>>>>> $SPHERE_MWS $TOPO
>>>>>>>>>
>>>>>>>>> There are no parameters for this one; they are built in, apparently,
>>>>>>>>> so I'm not sure what could be going on.
>>>>>>>>>
>>>>>>>>> I'm stumped.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Nov 25, 2013, at 4:27 PM, Taosheng Liu <[email protected]> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Donna,
>>>>>>>>>> I've been using the preborder and postborder scripts to convert
>>>>>>>>>> files from FreeSurfer to Caret (hope you still remember I was
>>>>>>>>>> involved in early testing of these scripts). Things have been
>>>>>>>>>> working great. I haven't done this for a while, but recently I
>>>>>>>>>> changed computer and installed the current version of Caret and
>>>>>>>>>> these scripts, and there seems to be some difference in how the code
>>>>>>>>>> works. I just want to make sure this is expected behavior.
>>>>>>>>>> Specifically, when we run postborder script, it takes much longer.
>>>>>>>>>> It seems either the script or caret_command is doing more
>>>>>>>>>> iterations, because we now see files like this after the script
>>>>>>>>>> finishes:
>>>>>>>>>>
>>>>>>>>>> Human.FS040.L.SPHERICAL.73730.MWS.SPHERE_CYCLE144.coord
>>>>>>>>>>
>>>>>>>>>> There're a lot of files like this, with consecutive names from
>>>>>>>>>> CYCLE1 to CYCLE 144, whereas previously it only goes from CYCLE1 to
>>>>>>>>>> CYCLE4. My question is: is this expected behavior, or is there
>>>>>>>>>> something wrong in how we ran the scripts?
>>>>>>>>>> I've posted the result from the check_reg here
>>>>>>>>>> http://psychology.msu.edu/liulab/files/html_out/views.html
>>>>>>>>>>
>>>>>>>>>> They look just like before, but I'd like to confirm whether this is
>>>>>>>>>> normal.
>>>>>>>>>> Thank you very much,
>>>>>>>>>>
>>>>>>>>>> --Taosheng
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Taosheng Liu
>>>>>>>>>> Assistant Professor
>>>>>>>>>> Department of Psychology
>>>>>>>>>> Michigan State University
>>>>>>>>>> 316 Physics Road
>>>>>>>>>> East Lansing, MI 48824
>>>>>>>>>> PH: 517.432.6694
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> caret-users mailing list
>>>>>>>>>> [email protected]
>>>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>> _______________________________________________
>>>>>>>>> caret-users mailing list
>>>>>>>>> [email protected]
>>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>>> --
>>>>>>>> Taosheng Liu
>>>>>>>> Assistant Professor
>>>>>>>> Department of Psychology
>>>>>>>> Michigan State University
>>>>>>>> 316 Physics Road
>>>>>>>> East Lansing, MI 48824
>>>>>>>> PH: 517.432.6694
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> caret-users mailing list
>>>>>>>> [email protected]
>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>> _______________________________________________
>>>>>>> caret-users mailing list
>>>>>>> [email protected]
>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
>>>>>> [email protected]
>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>> --
>>>>> Taosheng Liu
>>>>> Assistant Professor
>>>>> Department of Psychology
>>>>> Michigan State University
>>>>> 316 Physics Road
>>>>> East Lansing, MI 48824
>>>>> PH: 517.432.6694
>>>>>
>>>>> _______________________________________________
>>>>> caret-users mailing list
>>>>> [email protected]
>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>> _______________________________________________
>>>> caret-users mailing list
>>>> [email protected]
>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>> --
>>> Taosheng Liu
>>> Assistant Professor
>>> Department of Psychology
>>> Michigan State University
>>> 316 Physics Road
>>> East Lansing, MI 48824
>>> PH: 517.432.6694
>>>
>>> _______________________________________________
>>> caret-users mailing list
>>> [email protected]
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>> _______________________________________________
>> caret-users mailing list
>> [email protected]
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
> --
> Taosheng Liu
> Assistant Professor
> Department of Psychology
> Michigan State University
> 316 Physics Road
> East Lansing, MI 48824
> PH: 517.432.6694
>
> _______________________________________________
> caret-users mailing list
> [email protected]
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
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