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Hi Anna, Did you remove BOTH the xml file AND the corresponding folder it points to? I think fslview flounders whenever there is an XML file that is pointing to something that isn't there.... certainly the paths specified in the XML file should make sense/be real. -Dianne On Wed, Feb 8, 2012 at 12:28 PM, Dzieciol, Anna <[log in to unmask]>wrote: > Hello Dianne, > > Thanks for your help. Removing Cerebellum atlas didn't fix the problem. I > also tried changing the .xml file to remove the extra slash, but this > didn't work either: > > ** ERROR (nifti_image_read): failed to find header file for > '/usr/share/fsl/4.1/data/atlases/Cerebellum/Cerebellum-MNIflirt-prob-1mm' > ** ERROR: > nifti_image_open(/usr/share/fsl/4.1/data/atlases/Cerebellum/Cerebellum-MNIflirt-prob-1mm): > bad header info > Error: failed to open file > /usr/share/fsl/4.1/data/atlases/Cerebellum/Cerebellum-MNIflirt-prob-1mm > > Now the extra slash disappeared from the error message, but the problem > persists. > > I can open the Cerebellum-MNIflirt-prob-1mm (or other atlas files) in > MRICron but fslview won't let me go into the folder. > > I think that it may have something to do with the symbolic links that are > created for these files. For example the Cerebellum atlas .xml file links > to -> ../../../data/bangor-cerebellar-atlas/Cerebellum_MNIflirt.xml , which > doesn't exist. Is it supposed to be like that? > > > All the best, > > Anna > > > > Date: Tue, 7 Feb 2012 11:11:58 -0700 > From: Dianne Patterson <[log in to unmask]> > Subject: Re: No atlases showing in fslview > > I'd try removing the offending Cerebellum atlas....though I suspect the > problem is the path specified: > > /usr/share/fsl/4.1/data/atlases//Cerebellum/Cerebellum-MNIflirt-prob-1mm > (note // between atlases and Cerebellum).... > so you might take a look in the Cerebellum.xml file and change the path to > the file flirt file in question.. > > -Dianne > > On Tue, Feb 7, 2012 at 6:03 AM, Dzieciol, Anna > <[log in to unmask]>wrote: > > > Dear all,**** > > > > ** ** > > > > I’m using Ubuntu 11.04. I downloaded FSL from Synaptic and added > > fsl-atlases from NeuroDebian. The atlases seem to have installed > correctly: > > **** > > > > ** ** > > > > ls $FSLDIR/data/atlases**** > > > > ** ** > > > > bin HarvardOxford-Subcortical.xml MNI**** > > > > Cerebellum JHU MNI.xml**** > > > > Cerebellum_MNIflirt.xml JHU-labels.xml Talairach**** > > > > Cerebellum_MNIfnirt.xml JHU-tracts.xml > Talairach.xml** > > ** > > > > HarvardOxford Juelich Thalamus**** > > > > HarvardOxford-Cortical.xml Juelich.xml > Thalamus.xml*** > > * > > > > ** ** > > > > However, when I open fslview I get an error message:**** > > > > ** ERROR (nifti_image_read): failed to find header file for > > > '/usr/share/fsl/4.1/data/atlases//Cerebellum/Cerebellum-MNIflirt-prob-1mm' > > **** > > > > ** ERROR: > > > nifti_image_open(/usr/share/fsl/4.1/data/atlases//Cerebellum/Cerebellum-MNIflirt-prob-1mm): > > bad header info**** > > > > Error: failed to open file > > > /usr/share/fsl/4.1/data/atlases//Cerebellum/Cerebellum-MNIflirt-prob-1mm** > > ** > > > > ** ** > > > > I also get ‘Failed to initialise Atlas Widget’ in the GUI**** > > > > ** ** > > > > The atlas toolbar comes up empty (with no atlases listed) and when I > click > > on the atlases or structures button the program crashes:**** > > > > ** ** > > > > fslview: /usr/include/boost/smart_ptr/shared_ptr.hpp:418: T* > > boost::shared_ptr< <template-parameter-1-1> >::operator->() const [with > T = > > AtlasGroup]: Assertion `px != 0' failed.**** > > > > Aborted**** > > > > ** ** > > > > I hope you can help me to sort this out.**** > > > > ** ** > > > > Anna**** > > > > ** ** > > > > ** ** > > > > _____________**** > > > > *Anna Dzieciol* > > > > *PhD student* > > > > *DCNU* > > > > *UCL Institute of Child Health* > > > > *020 7905 **2314* > > > > *[log in to unmask]* > > > > ** ** > > > > > > -- > Dianne Patterson, Ph.D. > Research Scientist > [log in to unmask] <[log in to unmask]> > University of Arizona > Speech and Hearing Science 314 > 1131 E 2nd Street, Building #71 > (Just East of Harvill) > 621-9877 > ============== > If you write me (expecting an answer) and I don't respond within a > day, then the UAConnect System has probably lost your message. > You can always write me at [log in to unmask], > because gmail actually works. > ============== > “You tend to get told that the world is the way it is, but life can be much > broader once you discover one simple fact; and that is that everything > around you that you call life was made up by people no smarter than you… > Once you learn that, you’ll never be the same again.” > -Steve Jobs > > ------------------------------ > > -- Dianne Patterson, Ph.D. Research Scientist [log in to unmask] <[log in to unmask]> University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) 621-9877 ============== If you write me (expecting an answer) and I don't respond within a day, then the UAConnect System has probably lost your message. You can always write me at [log in to unmask], because gmail actually works. ============== “You tend to get told that the world is the way it is, but life can be much broader once you discover one simple fact; and that is that everything around you that you call life was made up by people no smarter than you… Once you learn that, you’ll never be the same again.” -Steve Jobs