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Thanks Janine, it was a good idea. However, I tried and it didn't solve my
problem.

Do you FSL experts have more suggestions?


Best,

Daniela

2018-01-18 17:39 GMT+00:00 Janine Bijsterbosch <
[log in to unmask]>:

> Hi,
>
> Yep, they look fine to me. Perhaps matlab can’t find randomise. You can
> fix this as explained on the very bottom of this link:
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/MacOsX#Using_
> FSL_MATLAB_libraries, or potentially by opening matlab from the command
> line.
>
> Cheers,
>
> Janine
>
>
> On 18 Jan 2018, at 17:32, Daniela Valério <[log in to unmask]
> COM> wrote:
>
> Hi Janine,
>
> I think that these 2 files are okay. However, I'm sending them attached to
> you can take a look.
>
>
> Thanks,
>
> Daniela
>
> 2018-01-18 17:25 GMT+00:00 Janine Bijsterbosch <
> [log in to unmask]>:
>
>> Hi Daniela,
>>
>> It looks like randomise didn’t run correctly. Do your design_10.mat and
>> design_10.con files look appropriate (i.e. do they contain EVs and
>> contrasts)? The ncon variable is set based on the number of randomise
>> outputs (which is the same as the number of contrasts), and should
>> therefore never be empty.
>>
>> Cheers,
>>
>> Janine
>>
>>
>> On 18 Jan 2018, at 17:00, Daniela Valério <[log in to unmask]
>> COM> wrote:
>>
>> Dear FSL experts,
>>
>> I started recently to do functional connectivity with FSL Nets. And, I
>> stopped in an error that I don't have any idea how to solve it.
>>
>>  When I ran my_nets code, I have this problem:
>>
>> "Error using figure
>> Value must be a 4 element vector
>>
>> Error in nets_glm (line 48)
>> figure('Position', [100 100 600*ncon 500]);
>>
>> Error in my_nets (line 72)
>> [p_uncorrected,p_corrected]=nets_glm(netmats1,'design_10.mat','design_10.con',1);
>>  % returns matrices of
>> 1-p"
>>
>> In my nets_glm code, I have the "ncon variable" empty. I think that the
>> problem occurs in line 38 in the function randomize.
>>
>> save_avw(reshape(netmats',XXX,1,1,TTT),fname,'f',[1 1 1 1]);
>>  *system(sprintf('randomise -i %s -o %s -d %s -t %s -x --uncorrp -n
>> %d',fname,fname,des,con,nperms));*
>>
>> % how many contrasts were run?
>> [grot,ncon]=system(sprintf('imglob %s_vox_corrp_tstat*.* | wc
>> -w',fname));
>> ncon=str2num(ncon);
>>
>> if view==1
>> figure('Position', [100 100 600*ncon 500]);
>> end
>>
>>
>> I tried to diagnose the error and I identified that the temporary image
>> that is necessary to randomize has the size 169 1 1 10, where 169 is my
>> time series dimension and 10 is my number of subjects.
>>
>> I don't know if this helps, but I have the FSL version 5.09.
>>
>>
>> Thanks in advance for any help!
>>
>> Best,
>>
>> Daniela Valério
>>
>>
>>
>> -----
>> Dr Janine Bijsterbosch
>> Postdoctoral Researcher
>> FMRIB Centre, University of Oxford
>> John Radcliffe Hospital
>> Oxford, United Kingdom
>> [log in to unmask]
>>
>>
> <design_10.con><design_10.mat>
>
>
> -----
> Dr Janine Bijsterbosch
> Postdoctoral Researcher
> FMRIB Centre, University of Oxford
> John Radcliffe Hospital
> Oxford, United Kingdom
> [log in to unmask]
>
>