Great, now I understand. Thanks again!

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Mark Jenkinson
Sent: Wednesday, January 23, 2008 9:42 AM
To: [log in to unmask]
Subject: Re: [FSL] missing tsplot and reg_standard FEAT output folders

Hi,

Glad that this seems to be working now.

The reg_standard folder gets created automatically
when you run higher-level analysis.
Is that what you are doing?
You won't see it after just first-level analysis.

All the best,
	Mark


On 23 Jan 2008, at 16:30, Sarah Andersen wrote:

> Thanks for the encouragement to reinstall. I'm not sure what it  
> corrected,
> but it is now creating the timeplots and the correct images in the
> post-stats report!
>
> One quick question, if I designate a main structural image and a  
> standard
> MNI reference image to register the data to, should it also create a
> reg_standard/stats folder with the stats resampled into standard  
> space? This
> seems to be the only thing that I am still missing. Or is this  
> something
> that needs to specifically designated?
>
> Thanks again for all the help,
> Sarah
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On  
> Behalf
> Of Steve Smith
> Sent: Monday, January 21, 2008 7:53 AM
> To: [log in to unmask]
> Subject: Re: [FSL] missing tsplot and reg_standard FEAT output folders
>
> 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
> ---------------------------------------------------------------------- 
> -----
>