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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