Hi,
FSL 4.1.2 should have the low-variance masking patch in - could
you upload your data to:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
so we can confirm what the problem is?
Many Thanks
Matthew
> Hi there,
>
> My colleague emailed back in December with some problems he was having
> with FEAT (email thread pasted below). Matthew concluded that the
> problem originated with a difference in how input data with low
> variance is masked between 4.0 and 4.1, and sent us a corrected
> film_gls, which worked perfectly on our Mac OS X system. We have
> recently moved our data to a server running Red Hat Linux Ver 4.5
> (64bit). We installed the most recent version of FSL (4.1.2), and the
> same problem has popped up again (see attached image), so perhaps this
> fix was omitted from the most recent version?
>
> We would really appreciate it if you could send/make available the
> same fix for our new system.
>
> Thanks a million,
> Clare
>
>
> On 18 Dec 2008, at 13:33, Mennes, Maarten wrote:
>
>> Hi Matthew,
>>
>> thanks for getting back at me. 'Good' for me to know its only a bug
>> and not me doing something wrong.
>> I'm using Mac OSX 10.5 (leopard) running on an intel core.
>>
>> Thanks again!
>> Maarten
>>
>>
>>
>> -----Original Message-----
>> From: Matthew Webster [mailto:[log in to unmask]]
>> Sent: Thu 12/18/2008 7:58 AM
>> To: Mennes, Maarten
>> Subject: Re: Analysis inconsitencies between FSL4.0 and FSL4.1.2
>>
>> Hi,
>> I've had a look at your data - the bug comes from a difference in
>> how input data with low variance is masked between 4.0 and 4.1. We'll
>> be issuing a patch in January, but I can send you a corrected
>> film_gls
>> binary before then if you let me know what platform you are using...
>>
>> Many Regards
>>
>> Matthew
>>
>>
>>
>>> From: "Mennes, Maarten" <[log in to unmask]>
>>> Date: 15 December 2008 15:29:24 GMT
>>> To: "Steve Smith" <[log in to unmask]>
>>> Subject: RE: Analysis inconsitencies between FSL4.0 and FSL4.1.2
>>>
>>> Dear Professor,
>>>
>>> the file is uploaded, the upload ID is 334053 and the filename is
>>> CSC-FSL412.tar.gz
>>>
>>> Thanks for the quick response!
>>> Maarten
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Steve Smith [mailto:[log in to unmask]]
>>> Sent: Mon 12/15/2008 10:09 AM
>>> To: Mennes, Maarten
>>> Subject: Re: Analysis inconsitencies between FSL4.0 and FSL4.1.2
>>>
>>> Hi - I thought maybe this was down to a chance in the masking - but
>>> no, LOADS of voxels are zero in the latest version - clearly a
>>> problem
>>> here. Could you upload the full input data and output FEAT directory
>>> (for just 4.1.2 is enough) and we'll 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 Dec 2008, at 15:00, Mennes, Maarten wrote:
>>>
>>>>
>>>> Dear Professor Smith,
>>>>
>>>> I recently started working with FSL when moving to the NYU Child
>>>> Study Center, having worked with SPM before. In getting to know the
>>>> FSL way on doing fMRI analysis I found a strange difference between
>>>> results produced with FSL4.0 and FSL4.1.2. I had installed the
>>>> latest version on my computer but could not produce the same
>>>> results
>>>> on some sample data from the lab as others had produced before. It
>>>> turned out that doing the same analysis with FSL4.0 did return the
>>>> same results, leaving us puzled about a possible cause for this.
>>>>
>>>> What seems to happen in the FSL 4.1.2 results is that in the zstat
>>>> maps some voxels are set to 0, while others just keep their z-
>>>> value.
>>>> The setting to 0 seems to happen at random. Is this something that
>>>> you are aware of?
>>>>
>>>> I have attached the design files and zstat maps of the FSL 4.0 and
>>>> FSL 4.1.2 analysis. If you need additional information please let
>>>> me
>>>> know.
>>>>
>>>> Sincerely,
>>>> Maarten Mennes
>>>>
>>>> ------------------------------------------------------------
>>>> This email message, including any attachments, is for the sole use
>>>> of the intended recipient(s) and may contain information that is
>>>> proprietary, confidential, and exempt from disclosure under
>>>> applicable law. Any unauthorized review, use, disclosure, or
>>>> distribution is prohibited. If you have received this email in
>>>> error
>>>> please notify the sender by return email and delete the original
>>>> message. Please note, the recipient should check this email and any
>>>> attachments for the presence of viruses. The organization accepts
>>>> no
>>>> liability for any damage caused by any virus transmitted by this
>>>> email.
>>>> =================================
>>>> <
>>>> design_FSL40
>>>> .fsf><design_FSL412.fsf><zstat1_FSL40.nii.gz><zstat1_FSL412.nii.gz>
>>>
>
>
> --
> A.M. Clare Kelly, Ph.D.,
> Postdoctoral Research Fellow,
> NYU Child Study Center,
> 215 Lexington Ave, 14th Floor,
> New York, NY 10016
> <correlations.png>
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