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Subject:

AW: [FSL] Stimulus with long duration & Arterial Spin Labeling

From:

Andreas Bartsch <[log in to unmask]>

Reply-To:

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

Date:

Thu, 29 Jul 2004 21:44:22 +0200

Content-Type:

text/plain

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text/plain (1 lines)

Hi,

w/r to 2):

ASL-data can be hard to model. I have been quite happy applying melodic to single-subject ASL-data. You can high-pass filter but be aware of the appropriate cutoff. Furthermore, you want to derive your mask from the original EPI but obviously not the difference images. I have had some datasets were I kept the entire FoV for inclusion to get meaningful results. Christian has recently extended PICA to multiple run / subjects based on a tensor approach (see HBM abstracts) but as yet this is not available in the current fsl version. So as a first trial, you may want to go ahead using the hypothesis-driven approach as indicated by Mark.

Cheers-

Andreas

 

-----Original Message-----

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]On

Behalf Of Mark Woolrich

Sent: donderdag 29 juli 2004 13:32

To: [log in to unmask]

Subject: Re: [FSL] Stimulus with long duration & Arterial Spin Labeling





Anda,



> 1) What measures can we take to avoid several confounds that come into

> issue with such long duration:

> motion correction ...drift of signal etc... refractoriness of signal...

etc.



- nothing I can think of other than rely upon there being enough CNR to

overcome the huge amounts of noise at low frequency in FMRI. I think you

will really struggle to get anything out. Anybody else out there?



> 2) Can data, derived from Arterial Spin Labeling (ASL) be analysed with

> FSL ??



- you should be able to use FSL to do a basic analysis ASL data. However,

this it is not an automated process at the moment. You will want to

(maybe after slice timing) use motion

correction on the original EPI data. Then difference the control and tag

scans to create the ASL dataset for analysis. Then proceed with spatial

smoothing and FSL stats. However, you should turn OFF high-pass filtering

and prewhitening.



Cheers, Mark.



Mark Woolrich.



Oxford University Centre for Functional MRI of the Brain (FMRIB),

John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.



Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich



On Thu, 29 Jul 2004, Anda van Stegeren wrote:



> Hi there,

>

> 2 questions: for an fMRI study we want to present films with long duration:

> e.g. 4 minutes with the obvious purpose to find out if activation during

> film is higher/lower than baseline.

>

> 1) What measures can we take to avoid several confounds that come into

> issue with such long duration:

> motion correction ...drift of signal etc... refractoriness of signal... etc.

>

> even more basic: can we use FSL for this, which I certainly hope we can.

>

> 2) Can data, derived from Arterial Spin Labeling (ASL) be analysed with

> FSL ??

>

> anyone experience with these issues ??? THanks a lot,

> Anda van Stegeren

>

> University of Amsterdam

> The Netherlands

> [log in to unmask]

>



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