hi Christain:
More over. I want to run my nifti data on a Mac computer, but do the ICA data analysis on another Windows computer. Those matlab scripts in $FSLDIR/etc/matlab I have already moved them in the correct path on the Windows computer.
But when I ran the read_avw( ) function, there was mistakes. I check the source code, there is a line in read_avw file is:
system(['sh -c "FSLOUTPUTTYPE=NIFTI_PAIR; export FSLOUTPUTTYPE; $FSLDIR/bin/avwmaths ', fname, ' ', tmpname,'"']);
and I think the matlab scripts is default for the case that both FSL and these scripts are on the same computer. Plus, I saw there is a file named "melodic_ICA.nii.gz" in my results folder. I am not sure if we still need the command line above to generate another nifiti file?
My real question is: How can modify these script so that I can do my ICA data analysis on a different computer? Can I generate nifti format file of ICA results on my Mac(if needed), and doin the ICA data analysis using my Windows?
Thanks
XC
****************************************
Xuelin Cui
Department of Electrical Engineering
University of Hawaii-Manoa
Honolulu HI 96822
Tel: 1-808-349-0983
Email: [log in to unmask]
****************************************
----- Original Message -----
From: Christian Beckmann <[log in to unmask]>
Date: Thursday, June 28, 2007 3:14 pm
Subject: Re: [FSL] How to find the exact numeric value of those spatial IC maps in MELODIC?
To: [log in to unmask]
> Hi,
>
> simply use read_avw (in $FSLDIR/etc/matlab) to load the entire 4d
> file into matlab. You can then check each voxels value in each map
>
> easily:
>
> data=read_avw('blah.ica/melodic_IC');
> data(20,20,10,3)
>
> ans = some value
>
> This then is the value of voxel 20,20,10 in IC map 3. If you want
> to
> mask out the background voxels then you can do the following
>
> data = read_avw('test');
> mask=read_avw('mask');
> mask=reshape(mask,prod(size(mask)),1)' > 0;
> data=reshape(data,prod(size(mask)),prod(size(data))/prod(size(mask)))';
> data=data(:,mask);
>
> data then is a 2d matrix (#ICs x #voxels). If you only want to
> find
> out about a small number of values you can simply load melodic_IC
> to
> fslview and click on the voxels of interest.
> hope this helps
> christian
>
>
> On 28 Jun 2007, at 01:45, Xuelin Cui wrote:
>
> > Dear all:
> >
> > As we know, ICA decomposes the fMRI data in to a time course
> matrix
> > and a spatial map matrix. Those time course values are easy to
> see
> > if we simply click the time course picture on the html file.
> Also,
> > we can see *.txt files, which is the time course data, in the
> folder.>
> > I just wonder are there a similar txt files for spatial map?
> What
> > if I am interested in the exact intensity of each spatial map? I
> am
> > think of using Matlab to read those spatial map, but the problem
> is
> > those IC maps are put together, and there are lots of marginal
> area
> > on the picture that is not needed. So, is there a way to find
> out
> > the exact value of each independent spatial maps?
> >
> > Thanks a lot
> >
> > Xuelin
> >
> > ****************************************
> > Xuelin Cui
> > Department of Electrical Engineering
> > University of Hawaii-Manoa
> > Honolulu HI 96822
> >
> > Tel: 1-808-349-0983
> > Email: [log in to unmask]
> > ****************************************
>
> ____
> Christian F. Beckmann
> University Research Lecturer
> Oxford University Centre for Functional MRI of the Brain (FMRIB)
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
> [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
> tel: +44 1865 222551 fax: +44 1865 222717
>
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