Hi again, 
I could use AFNI too. Did you do partial volume correction? How to do it in AFNI?



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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Christine Zakrzewski [[log in to unmask]]
Sent: Friday, November 18, 2011 3:49 AM
To: [log in to unmask]
Subject: Re: [FSL] Partial volume correction

Hi. I am an AFNI user myself, therefore, excuse my initial lack of FSL specific information.
Check out this link, http://fsl.fmrib.ox.ac.uk/analysis/dualreg/dualreg_poster.pdf, which describes using multi-subject independent coponents analysis and dual regression on resting state fMRI data.
It seems you will use MELODIC to perform a concatenated independent component analysis, on multiple subjects, and then use dual regression to identify exactly which datasets (in terms of spatial extent and associated timecourse) in which these components occur.
Hope this is helpful.

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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Xiaozhen Li [[log in to unmask]]
Sent: Thursday, November 17, 2011 1:38 PM
To: [log in to unmask]
Subject: Re: [FSL] Partial volume correction

Hi,
I read the documents and course lecture. But I didn't find any detail about partial volume correction. Could you tell me in detail?
Thank you very much!

Sent from my iPhone

On 17 Nov 2011, at 19:12, "Christine Zakrzewski" <[log in to unmask]> wrote:

> Hi. I would refer to lectures and documentation from the FSL course to augment your understanding.
>
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Xiaozhen Li [[log in to unmask]]
> Sent: Thursday, November 17, 2011 12:51 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Partial volume correction
>
> Sorry, I don't understand. I use Glm to design matrix. It works well for covariates with age and gender. But it does not work with partial volume correction. How to do it?
> Thanks again!
>
> Sent from my iPhone
>
> On 17 Nov 2011, at 18:45, "Christine Zakrzewski" <[log in to unmask]> wrote:
>
>> Multiple regression will control for multiple covariates.
>>
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Xiaozhen Li [[log in to unmask]]
>> Sent: Thursday, November 17, 2011 9:04 AM
>> To: [log in to unmask]
>> Subject: [FSL] Partial volume correction
>>
>> Dear FSL experts,
>>
>> I try to do partial volume correction for ASL data in fsl.  When I put the GW/WM ratios 4D images into the Glm to design matrix, there is an error report '#5 out of bound ... RBG ...'. I also try the GM images, got the same error report.
>>
>> Which one should I use, GM/WM ratios or just GM? Do I need demean the image?
>>
>> Otherwise, is there any other methods to do partial volume correction, covariates with age and gender at the same time?
>>
>> Thanks a lot!
>>
>> Best Regards,
>> Xiaozhen
>>
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