Hi - yes, it might be best to reinstall VMware and FSL from scratch,
following the installation instructions as much as possible (and let
Duncan know if it's not for any reason). Otherwise, if you would like
to upload a complete copy of the failed FEAT output directory, we can
take a look:
Please upload the files in a single compressed tarfile to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
And then email me the upload ID.
Cheers.
On 15 Jan 2008, at 15:49, Sarah Andersen wrote:
> Thanks for the reply Mark,
>
> I am logging in as the root user, mainly because I was concerned about
> permissions being an issue. Would it be safer to log in as fsl user
> and
> create the .feat folders that way?
>
> Here is how I installed VM and FSL: I used the online downloading
> instructions and followed them as exactly as I could--I am using a
> Windows
> Vista machine. I used the link to the VMware Player version 2
> download and
> installed it. There were no issues, although I have updated it
> occasionally.
> (When it's a kernel update, I've used the instructions from the FSL
> website
> to also update the vmware-tools.)
> There was something a bit odd with the FSL download. The webpage
> talked
> about putting the FSLvm [32bit] install in a folder called Virtual
> Machines
> that should have been created by the VMware Player. This wasn't
> created, so
> I made the folder myself. The FSLvm install also allowed me to open
> the
> VMware player, but FSL itself didn't work within it (eg the "sh
> fsl_installer.sh" command came back with an error). So I downloaded
> FSL
> through the FSL Downloads page, choosing the Linux CentOS5 32bit
> version.
> Once I used the tar command listed in the "Installing on Linux" page
> to
> uncompress and untar the download and configured the path so that it
> was set
> to the download, it seemed to work fine. I ran the FEEDS on it and
> it said
> that there were no errors. Additionally, I have been using the BET,
> FLIRT,
> and FSLview utilities within FSL without a problem.
>
> I hope this helps. Is there an obvious error in my installation
> method?
> Would it be worthwhile at this point to just start over and re-
> install both
> the VMware player and FSL? Or do you think that this is an issue with
> running FEAT in a virtual environment?
>
> I have also attached the output of "fslerrorreport" in case the error
> message there is helpful.
>
> I really appreciate your help!!
>
> sarah
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Mark Jenkinson
> Sent: Monday, January 14, 2008 3:08 PM
> To: [log in to unmask]
> Subject: Re: [FSL] missing tsplot and reg_standard FEAT output folders
>
> Dear Sarah,
>
> Feat should automatically produce all the time-series plots for you.
> There is no need to run tsplot manually.
>
> It sounds like your FSL installation or VM is broken in some way.
> I am not sure exactly what is wrong.
> Did you follow the installation instructions for the FSL VM exactly?
> I note from your previous email that your .feat folders are created
> as root. Are you logging in as root or as the fsl user?
>
> Any other information you can give us about how you installed
> your VM and fsl or about the errors would be helpful.
>
> All the best,
> Mark
>
>
>
>
> On 14 Jan 2008, at 21:59, Sarah Andersen wrote:
>
>> Dear FSLers,
>> As someone new to FSL, I have been working through the tutorial and
>> manuals to help my understanding of FEAT. However, I have run
>> across the same issue each time I run FEAT. This happens for both
>> the tutorial av data (from the fsl_course_data tarball) and my own
>> fMRI data, so I believe it isn't a problem with data corruption.
>> When I check my output against the diagram of the expected FEAT
>> output in the online manual (http://www.fmrib.ox.ac.uk/fsl/feat5/
>> output.html), I don't have either a tsplot or a reg_standard/stats/
>> folder created. Does this mean that there was an error in my
>> analysis somewhere? Or do you need to create these on your own by
>> using the tsplot command and the renderhighres commands?
>> Additionally, the html FEAT report post-stats section is lacking
>> any time series plots of the data vs. the model. While the zstat
>> and thresholded zstat images are still created and usable, I am
>> concerned that they may not be reliable given this error.
>>
>> This may not be relevant to my issue, but I am running FSL v4.0 in
>> a virtual environment with the VMware player recommended on the
>> website.
>>
>> Thanks in advance,
>> Sarah
>>
>> Sarah Andersen
>> Research Specialist
>> Dept. of Neurology
>> Dept. of Speech, Language, and Hearing Sciences
>> (520) 621-9878
>> [log in to unmask]
>>
> <fsl_R0dK9n.gz>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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