Hi,
most certainly you need to include the neurodebian repository in your
"sources.list", i.e., the list of servers your Lucid Lynx gets its
software from. Simply add the following lines to your sources.list
manually
deb http://neuro.debian.net/debian data main contrib non-free
deb http://neuro.debian.net/debian lucid main contrib non-free
or follow the instructions on the neuro.debian.net - homepage on how
to do it via command line. You can also enter the lines above into the
respective fields in synaptic, if you go via GUI. Ask for local help,
if necessary. Then you should be fine, all dependencies should be
accounted for. For me, Ubuntu (11.04 in my case, but had 10.4 LTS
before) and neurodebian work like a charm!
Best regards,
Cornelius
On Mon, Nov 21, 2011 at 4:00 PM, Olga Grigorieva <[log in to unmask]> wrote:
> Hi, Cornelius,
> thank you for your response. As I checked the downloaded files, it turns
> out, that fsl-atlases was not downloaded. As a matter of fact, fsl-atlases
> package is not available on the download page (from packages.ubuntu.com). I
> have also searched for this package on neuro.debian.net, and "There are no
> official Ubuntu packages available." message comes up. There is a non-free
> dataset, that I can download, however, I get the following error: "Error:
> Dependency is not satisfiable: fsl-harvard-oxford-atlases".
> One more thing, that I have noticed about the downloaded files (for the
> fsl-4.1 files), is that there is also an error message, shown by the package
> installer: "Error: Dependency is not satisfiable: libnifti2"
> Any thoughts on what to do in this situation?
> Sincerely,
> Olga
>
> On Tue, Nov 15, 2011 at 4:37 PM, Cornelius Werner
> <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> maybe an obvious thing, but did you install "fsl-atlases"?
>> Which repositories are you using? I recommend the "neurodebian" ones
>> (neuro.debian.net).
>> Cheers
>> Cornelius
>>
>>
>> On Tue, Nov 15, 2011 at 8:32 PM, Olga Grigorieva <[log in to unmask]>
>> wrote:
>> > Dear FSL support tech:
>> > I am installing FSL on Ubuntu (lucid, 10.04.03, amd 64), and I have run
>> > into
>> > a problem. I have used synaptic in order to install fsl, fsl-doc,
>> > fslview
>> > and fslview-doc. Both programs do run, the GUI opens up and I can view
>> > my
>> > images. However, when I try to use flirt or fnirt, when the standard
>> > image
>> > is needed, the process the following error appears:
>> > ** ERROR (nifti_image_read): failed to find header file for
>> > '/usr/share/fsl/data/standard/MNI152_T1_2mm_brain'
>> > ** ERROR:
>> > nifti_image_open(/usr/share/fsl/data/standard/MNI152_T1_2mm_brain): bad
>> > header info
>> > Error: failed to open file
>> > /usr/share/fsl/data/standard/MNI152_T1_2mm_brain
>> > ERROR: Could not open image
>> > /usr/share/fsl/data/standard/MNI152_T1_2mm_brain
>> > Image Exception : #22 :: Failed to read volume
>> > /usr/share/fsl/data/standard/MNI152_T1_2mm_brain
>> > terminate called after throwing an instance of
>> > 'RBD_COMMON::BaseException'
>> > Aborted
>> > Finished
>> > I have searched the whole computer for the standard MNI template files,
>> > and
>> > those could not be found anywhere.
>> > I have also downloaded FEEDS and started the ./RUN all process. However,
>> > it
>> > was taking too long (I left it running overnight, the process has run
>> > for
>> >>1279 minutes). So, there is no output from FEEDS.
>> > Please, help to resolve this issue.
>> > All my best,
>> > Olga Grigorieva
>> > PhD graduate student
>> > Department of Biophysics
>> > The Ohio State University
>> > [log in to unmask]
>> >
>>
>>
>>
>> --
>> Cornelius Werner
>> cornelius.werner<at>gmail.com
>
>
--
Cornelius Werner
cornelius.werner<at>gmail.com
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