hi Christian:
I echoed the $FSLDIR in my terminal, and it returned right path. But still, the matlab scripts gave such mistake infornmation:
system(['sh -c "FSLOUTPUTTYPE=NIFTI_PAIR; export FSLOUTPUTTYPE; $FSLDIR/bin/avwmaths ', fname, ' ', tmpname,'"']);
>>"sh; line 1: /bin/avwmaths: No such file or directory"
How can I be sure that my environment variables are totally right?
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, July 4, 2007 4:21 am
Subject: Re: [FSL] How to find the exact numeric value of those spatial IC maps in MELODIC?
To: [log in to unmask]
> again you don't have FSL installed correctly - you need to have
> FSLDIR set in your environment
> hope this helps
> Christian
>
>
> On 29 Jun 2007, at 03:07, Xuelin Cui wrote:
>
> > Also, when I was running the matlab scripts on the Mac, on which
>
> > the FSL is installed, I have some mistakes happening. I traced
> the
> > program, the mistake happened at:
> > system(['sh -c "FSLOUTPUTTYPE=NIFTI_PAIR; export FSLOUTPUTTYPE;
> > $FSLDIR/bin/avwmaths ', fname, ' ', tmpname,'"']);
> > The Matlab command windows shows"sh; line 1: /bin/avwmaths: No
> such
> > file or directory". I thereafter checked the /bin/ folder, and
> ther
> > are avwmaths folder and files in there. I am just confused on
> how
> > should I fix this problem.
> >
> > 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]
> > ****************************************
> >
> > ----- 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
> >>
>
> ____
> 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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