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FSL  March 2009

FSL March 2009

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Subject:

Re: FILM_GLS and low variance data

From:

Clare Kelly <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 11 Mar 2009 11:29:06 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (167 lines)

Sorry about that - I just uploaded the right data
(low_var_problem-RIGHTONE.tar.gz) - the ref number is 923685

Thanks!
Clare

On Wed, Mar 11, 2009 at 7:01 AM, Matthew Webster
<[log in to unmask]> wrote:
> 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>
>



-- 
A.M. Clare Kelly, Ph.D.,
Postdoctoral Research Fellow,
NYU Child Study Center,
215 Lexington Ave, 14th Floor,
New York, NY 10016

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