Error when do parcellation

[Qingyang Li]

Error msg are

INFO     : 2012-04-25 23:52:21,090 : main       : Working on parcellation: scale500

INFO     : 2012-04-25 23:52:21,090 : main       : ========================

Exception occurred in traits notification handler.

Please check the log file for details.

Traceback (most recent call last):

  File "/home/neurobureau/cmp_dir//scripts/map_connectome.py", line 19, in <module>

    cmp.connectome.mapit(cmpgui)

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/cmp/connectome.py", line 78, in mapit

    stage.run( cobj )

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/cmp/stages/parcellation/maskcreation.py", line 669, in run

    create_roi()

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/cmp/stages/parcellation/maskcreation.py", line 153, in create_roi

    if brv['d5'] == 'left':

KeyError: 'd5'

What's the possible reason here? there is no such key in the dictionary?

How to fix the?

The connectome mapper I was using was downloaded from github the day before yesterday.

Thanks

Yang
------
Qingyang Li

Balance and focus.

[Qingyang Li]

Anyone knows about this?

Thanks!

Yang

[Qingyang Li]

Hi all,

I got another problem.

I downloaded CMP today from github and installed in on another server...

But when I run connectomemapper, I got the following error:

connectomemapper

Xlib:  extension "RANDR" missing on display "localhost:11.0".

Traceback (most recent call last):

  File "/home/neurobureau/mybin/epd/bin/connectomemapper", line 14, in <module>

    cmpgui.show()

  File "/home/neurobureau/.local/lib/python2.7/site-packages/cmp/gui.py", line 466, in show

    self.edit_traits(kind='livemodal')

  File "/usr/local/epd-7.0-2-rh5-x86_64/lib/python2.7/site-packages/enthought/traits/has_traits.py", line 2241, in edit_traits

    handler, id, scrollable, args )

  File "/usr/local/epd-7.0-2-rh5-x86_64/lib/python2.7/site-packages/enthought/traits/ui/view.py", line 429, in ui

    ui.ui( parent, kind )

  File "/usr/local/epd-7.0-2-rh5-x86_64/lib/python2.7/site-packages/enthought/traits/ui/ui.py", line 218, in ui

    self.rebuild( self, parent )

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/toolkit.py", line 133, in ui_livemodal

    ui_live.ui_livemodal( ui, parent )

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_live.py", line 73, in ui_livemodal

    ui_dialog( ui, parent, MODAL )

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_live.py", line 99, in ui_dialog

    ui.owner.init( ui, parent, style )

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_live.py", line 223, in init

    sw = panel( ui, window )

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_panel.py", line 349, in panel

    content[0], ui )

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_panel.py", line 523, in fill_panel_for_group

    create_panel )

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_panel.py", line 672, in __init__

    self.add_items(content, panel, self.sizer)

  File "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_panel.py", line 863, in add_items

    show_labels |= item.show_label

AttributeError: 'ShadowGroup' object has no attribute 'show_label'

I installed CMP several days ago on another server using the same procedure, but that one works (the two installation used the same EPD )

Any thoughts?

Thanks!

Yang

[Alessandra Griffa]

Sorry for this bug.
I fixed it and commit to github.
If you do not want to download again from github, replace 'd5' with 'dn_hemisphere' in cmp/stages/parcellation/maskcreation.py, line 153

Alessandra

[Hiro Mano]

Dear Ms. Alessandra

It seems same thing happened to me but the error output showed it's
already replaced '5d' with 'dn_hemisphere'
in "/usr/local/lib/python2.6/dist-packages/cmp/stages/parcellation/
maskcreation.py" in line 153 in my case.

Though It seems there is a difference btw Yang's case and my case in
the version of python, do I need to update python to 2.7?

Any comment will be appreciated.

================================================================

INFO : 2012-05-08 08:19:41,766 : main : Working on
parcellation: scale500
INFO : 2012-05-08 08:19:41,766 : main :
========================
ERROR : 2012-05-08 08:19:41,824 : main : Exception occured:
'dn_hemisphere'
ERROR : 2012-05-08 08:19:41,824 : main : Traceback (most
recent call last):
File "/usr/local/lib/python2.6/dist-packages/cmp/gui.py", line 66,
in object_run_changed
cmp.connectome.mapit(object)
File "/usr/local/lib/python2.6/dist-packages/cmp/connectome.py",

line 78, in mapit
stage.run( cobj )

File "/usr/local/lib/python2.6/dist-packages/cmp/stages/parcellation/
maskcreation.py", line 670, in run
create_roi()
File "/usr/local/lib/python2.6/dist-packages/cmp/stages/parcellation/

maskcreation.py", line 153, in create_roi

if brv['dn_hemisphere'] == 'left':
KeyError: 'dn_hemisphere'

================================================================

Thank you.

Hiro

On May 2, 6:24 am, Alessandra Griffa <alessandrag...@gmail.com> wrote:
> Sorry for this bug.
> I fixed it and commit to github.
> If you do not want to download again from github, replace 'd5' with
> 'dn_hemisphere' in cmp/stages/parcellation/maskcreation.py, line 153
>

> AlessandraOn Thu, Apr 26, 2012 at 6:06 AM, Qingyang Li <con...@gmail.com> wrote:
> > Error msg are
>
> > INFO     : 2012-04-25 23:52:21,090 : main       : Working on parcellation:
> > scale500
> > INFO     : 2012-04-25 23:52:21,090 : main       : ========================
> > Exception occurred in traits notification handler.
> > Please check the log file for details.
> > Traceback (most recent call last):
> >   File "/home/neurobureau/cmp_dir//scripts/map_connectome.py", line 19, in
> > <module>
> >     cmp.connectome.mapit(cmpgui)
> >   File
> > "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/cmp/connectome.py" ,
> > line 78, in mapit
> >     stage.run( cobj )
> >   File

> > "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/cmp/stages/parcell ation/maskcreation.py",

> > line 669, in run
> >     create_roi()
> >   File

> > "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/cmp/stages/parcell ation/maskcreation.py",

[Hiro Mano]

Dr. Yang

Have you already solved this issue?

Could you give me some advices?

Any comments will be appreciated.

Regards,

Hiro

On Apr 27, 8:45 am, Qingyang Li <con...@gmail.com> wrote:
> Hi all,
>
> I got another problem.
> I downloaded CMP today from github and installed in on another server...
> But when I run connectomemapper, I got the following error:
>
> connectomemapper
> Xlib:  extension "RANDR" missing on display "localhost:11.0".
> Traceback (most recent call last):
>   File "/home/neurobureau/mybin/epd/bin/connectomemapper", line 14, in
> <module>
>     cmpgui.show()
>   File "/home/neurobureau/.local/lib/python2.7/site-packages/cmp/gui.py",
> line 466, in show
>     self.edit_traits(kind='livemodal')
>   File

> "/usr/local/epd-7.0-2-rh5-x86_64/lib/python2.7/site-packages/enthought/trai ts/has_traits.py",

> line 2241, in edit_traits
>     handler, id, scrollable, args )
>   File

> "/usr/local/epd-7.0-2-rh5-x86_64/lib/python2.7/site-packages/enthought/trai ts/ui/view.py",

> line 429, in ui
>     ui.ui( parent, kind )
>   File

> "/usr/local/epd-7.0-2-rh5-x86_64/lib/python2.7/site-packages/enthought/trai ts/ui/ui.py",

> line 218, in ui
>     self.rebuild( self, parent )
>   File

> "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/toolki t.py",

> line 133, in ui_livemodal
>     ui_live.ui_livemodal( ui, parent )
>   File

> "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_liv e.py",

> line 73, in ui_livemodal
>     ui_dialog( ui, parent, MODAL )
>   File

> "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_liv e.py",

> line 99, in ui_dialog
>     ui.owner.init( ui, parent, style )
>   File

> "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_liv e.py",

> line 223, in init
>     sw = panel( ui, window )
>   File

> "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_pan el.py",

> line 349, in panel
>     content[0], ui )
>   File

> "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_pan el.py",

> line 523, in fill_panel_for_group
>     create_panel )
>   File

> "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_pan el.py",

> line 672, in __init__
>     self.add_items(content, panel, self.sizer)
>   File

> "/home/neurobureau/mybin/epd/lib/python2.7/site-packages/traitsui/wx/ui_pan el.py",

[Qingyang Li]

Hi Hiro,

I redownload CMP from github and did a reinstall. then everything is fine...

btw, I don't have a Dr. title :) and Yang is my first name.

hope this helps.

Yang

------
Qingyang Li

Balance and focus.

[Hiro Mano]

Mr. Qingyang Li

Thank you so much for your reply and sorry for my misunderstanding.

I'll try your way.

Hiro