Hi Michael,

You were right, it was not specific to ASL and I have fixed the problem. 

I want to use Melodic because I'm more interested in functional connectivity differences between groups rather than functional activation increases and decreases.

To test for group differences, can I run dual_regression as one does usually for resting-state fMRI? 

Are the resting ASL networks the same than the resting fMRI networks? Can I use Biswal's metaICA to identify them using fslcc?


2013/4/21 Michael Chappell <[log in to unmask]>
I cannot immediately see why that has failed, it doesn't look like something specific to ASL.However, I don't have a lot of experience of ASL with melodic - what are you trying to do that means you want to use melodic?


On 18 Apr 2013, at 14:26, maria estanqueiro <[log in to unmask]> wrote:

Dear Michael,

I also have resting-state pseudocontinous ASL data, which I was trying to analyze with Melodic by selecting the Perfusion subtraction option and Multiple concatenation approach.

I am very new to ASL preprocessing and have no idea whether I need to change any other options in the Melodic interface.

The error I show bellow came out. I checked in mi reg_standard/ folders and in fact no filtered_func_data were generated. I tried using featregapply my_directory -f and it didn't work either.

Do you know how to solve this?

Higher-level MELODIC

/maxim/software/fsl5/fsl/bin/featregapply /maxim/home/maria/FINAL/AD/1002/ASL/20100518_170013000001ep2dpcaslphys1002570425-1122s004a001_ASL.ica

/maxim/software/fsl5/fsl/bin/flirt -ref reg/standard -in reg/standard -out reg_standard/standard -applyisoxfm 4

/maxim/software/fsl5/fsl/bin/flirt -ref reg_standard/standard -in filtered_func_data -out frgrot_3IOVng -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float
Image Exception : #22 :: ERROR: Could not open image filtered_func_data
terminate called after throwing an instance of 'RBD_COMMON::BaseException'

/maxim/software/fsl5/fsl/bin/fslmaths reg_standard/filtered_func_data -Tstd -bin reg_standard/mask -odt char
Cannot open volume reg_standard/filtered_func_data for reading!

2013/4/18 Bhaswati Roy <[log in to unmask]>
Thank You so much for your help.

On Thu, Apr 18, 2013 at 4:38 PM, Michael Chappell <[log in to unmask]> wrote:
If you want to do a simple t-test between the two groups then you should be able to use FEAT and do a 'higher-level' analysis testing your CBF maps as the parameter estimates. This would then be the same procedure as a BOLD higher level analysis so you can consult that section of the help pages. Alternatively you can use the non-parametric method in randomise for the same job.
You might like to determine if the CBF images you are getting from your scanner are in absolute or relative units. If the latter then there could be some extra global scaling between individuals that is not purely perfusion differences.


On 15 Apr 2013, at 10:07, Bhaswati Roy <[log in to unmask]> wrote:

> Dear Sir,
> We have obtained CBF maps derived from 3D pseudocontinous ASL imaging from 20 controls and 20 patients. CBF maps are generated from the scanner itself. We want to generate maps showing regions where CBF values are different of patients than control. I am very much confused as to use which FSL tool for generating these maps.
> Thanks in advance
> Regards
> Bhaswati