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
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