hi all:
I ran MELODIC and generated some ICA results. I was trying to use the Matlab codes in the folder of /etc/matlab/ to read the spatial IC intensities.
I tried those matlab scripts in the /etc/matlab/ folder. But I had some mistakes when I was running the code. I traced the program step by step, and i found in the script of read_avw(fname), there is a line as follows:
system(['sh -c "FSLOUTPUTTYPE=NIFTI_PAIR; export FSLOUTPUTTYPE; $FSLDIR/bin/avwmaths ', fname, ' ', tmpname,'"']);
And, after this line, the variable "tmpname" is not valued with the path where the ICA result it is.
I am not not really familiar with bash command. But I guess this line mainly is trying to write the tempname with the value of fname. and I guess this bash command line is probably where my problem is caused. I use a FSL for Mac g5, 3.3.11. Does any one have any suggestion on how to fix the problem? Should I modify the bash command line? and, how?
Thanks a lot in advance
Xuelin
****************************************
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: Wednesday, June 27, 2007 9:14 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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