hi Christian:
Is the mask you mentioned the NifTI file with the file name 'mask' in the ICA results folder? If so, can you introduce a little bit about what kind mask it is? Also, what if I want to apply other kinds of masks on my data?
Thanks
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 2:22 pm
Subject: Re: [FSL] How to find the exact numeric value of those spatial IC maps in MELODIC?
To: [log in to unmask]
> try
>
> system('sh -c "echo $FSLDIR"')
>
> from within matlab. If it does not return the correct path then
> you'll need to change your local setup. Alternatively, simply
> replace
> $FSLDIR by the correct path in all the read_avw* and save_avw*
> file
> within $FSLDIR/etc/matlab
>
> hope this helps
> christian
>
> On 4 Jul 2007, at 03:25, Xuelin Cui wrote:
>
> > 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
> >>
>
> ____
> 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
>
