Hi Carles,
To clarify, are you choosing the File -> Add atlas menu option, and
then selecting one of the XML files in $FSLDIR/data/atlases/ ?
If this is the case, FSLeyes already knows about the atlases in
$FSLDIR/data/atlases - you can simply open the atlas panel (the
Settings -> Ortho View -> Atlas panel) to browse the FSL atlases. The
File -> Add atlas menu option is for adding new atlases (custom ones
that are not shipped with FSL), that FSLeyes is not yet aware of.
Cheers,
Paul
On 16/10/2018, cfalcon <[log in to unmask]> wrote:
> Dear Paul,
> Thanks for the answer.
>
> Removing the folder did not fix the error. The atlases can be read as images
> (.mni.gz), but not as .xlm so no labelling information is available
>
> My current fsleyes version is 0.22.6
>
> Carles
> _______________________
>
> Carles Falcon
> Neuroimaging Researcher, Physicist
> Neuroimaging Platform
> BarcelonaBeta Brain Research Center (BBRC)
> [log in to unmask] <mailto:[log in to unmask]>
> T. (+34) 93 316 09 90
> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=tel%3A%2B34%2520933%252016%252009%252090>
> C/ Wellington, 30
> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=https%3A%2F%2Fmaps.google.com%2F%3Fq%3DC%2F%2BWellington%2C%2B30%2B08005%2BBarcelona%26entry%3Dgmail%26source%3Dg>
> 08005 Barcelona
> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=https%3A%2F%2Fmaps.google.com%2F%3Fq%3DC%2F%2BWellington%2C%2B30%2B08005%2BBarcelona%26entry%3Dgmail%26source%3Dg>
> www.barcelonabeta.org
> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=http%3A%2F%2Fwww.barcelonabeta.org%2F>
> www.fpmaragall.org
> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=http%3A%2F%2Fwww.fpmaragall.org%2F>
>
>
> Aquest missatge i els seus annexos poden contenir informació confidencial i
> exclusiva per al destinatari. El seu contingut no constitueix un compromís
> per part de l'emissor. Si rep aquest missatge per error, si us plau
> elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent.
> Gràcies per la seva col·laboració. Este mensaje y sus anexos pueden contener
> información confidencial y exclusiva para el destinatario. Su contenido no
> constituye un compromiso por parte del emisor. Si recibe este mensaje por
> error, por favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al
> remitente. Gracias por su colaboración. This message and attachments may
> contain confidential and exclusive information intended only for the
> individual named. The content of this message does not imply any commitment
> by the sender. If you have received this e-mail by mistake, please delete it
> before reading or distributing and notify the sender. Thank you for your
> cooperation.
> Gràcies per estalviar paper. Gracias por ahorrar papel. Thanks for saving
> paper.
>
>
>
>
>> El 15 oct 2018, a les 12:24, cfalcon <[log in to unmask]> va
>> escriure:
>>
>> Dear all,
>> I get the following error message when trying to open any atlas with
>> fsleyes:
>>
>> MacOS/fsleyes
>> objc[15177]: Class FIFinderSyncExtensionHost is implemented in both
>> /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit
>> (0x7fff9cdc7c90) and
>> /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride
>> (0x11abbacd8). One of the two will be used. Which one is undefined.
>> ERROR status.pyc 164: reportIfError - Error loading atlas
>> specification: An error occurred loading the atlas specification
>> /Applications/fsl/data/atlases/JHU-labels.xml.
>> Traceback (most recent call last):
>> File "fsleyes_widgets/utils/status.pyc", line 160, in reportIfError
>> File "fsleyes/actions/loadatlas.pyc", line 75, in loadAtlas
>> File "fsl/data/atlases.pyc", line 225, in addAtlas
>> KeyError: 'An atlas with ID "jhu-labels" already exists'
>> Traceback (most recent call last):
>> File "fsleyes/actions/base.pyc", line 151, in wrapper
>> File "fsleyes/actions/base.pyc", line 129, in __call__
>> File "fsleyes/actions/loadatlas.pyc", line 47, in __loadAtlas
>> File "fsleyes/actions/loadatlas.pyc", line 75, in loadAtlas
>> File "fsl/data/atlases.pyc", line 225, in addAtlas
>> KeyError: 'An atlas with ID "jhu-labels" already exists'
>>
>> I reinstalled both fsl and fsleyes but the problem remains. Fsleyes works
>> fine except for this.
>> Any clue about how to fix the problem will be welcome. I am using
>> FSL5.0.10 on a Mac0S High Sierra 10.13.4.
>>
>> Thanks,
>>
>> Carles
>> _______________________
>>
>> Carles Falcon
>> Neuroimaging Researcher, Physicist
>> Neuroimaging Platform
>> BarcelonaBeta Brain Research Center (BBRC)
>> [log in to unmask] <mailto:[log in to unmask]>
>> T. (+34) 93 316 09 90
>> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=tel%3A%2B34%2520933%252016%252009%252090>
>> C/ Wellington, 30
>> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=https%3A%2F%2Fmaps.google.com%2F%3Fq%3DC%2F%2BWellington%2C%2B30%2B08005%2BBarcelona%26entry%3Dgmail%26source%3Dg>
>> 08005 Barcelona
>> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=https%3A%2F%2Fmaps.google.com%2F%3Fq%3DC%2F%2BWellington%2C%2B30%2B08005%2BBarcelona%26entry%3Dgmail%26source%3Dg>
>> www.barcelonabeta.org
>> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=http%3A%2F%2Fwww.barcelonabeta.org%2F>
>> www.fpmaragall.org
>> <https://barcelonabeta-dot-yamm-track.appspot.com/Redirect?ukey=1s_19_ZGi7b-bwSHj9kfPUVgZCr65-nTeheM_PpAT5KQ-0&key=YAMMID-00590388&link=http%3A%2F%2Fwww.fpmaragall.org%2F>
>>
>>
>> Aquest missatge i els seus annexos poden contenir informació confidencial
>> i exclusiva per al destinatari. El seu contingut no constitueix un
>> compromís per part de l'emissor. Si rep aquest missatge per error, si us
>> plau elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent.
>> Gràcies per la seva col·laboració. Este mensaje y sus anexos pueden
>> contener información confidencial y exclusiva para el destinatario. Su
>> contenido no constituye un compromiso por parte del emisor. Si recibe este
>> mensaje por error, por favor elimínelo sin revisarlo ni reenviarlo y
>> notifíquelo al remitente. Gracias por su colaboración. This message and
>> attachments may contain confidential and exclusive information intended
>> only for the individual named. The content of this message does not imply
>> any commitment by the sender. If you have received this e-mail by mistake,
>> please delete it before reading or distributing and notify the sender.
>> Thank you for your cooperation.
>> Gràcies per estalviar paper. Gracias por ahorrar papel. Thanks for saving
>> paper.
>>
>>
>>
>>
>
>
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