Hi Matthew,
No, I'm not able to run linkage on the example data. It reads the same error (the input character is not valid in Matlab statements…)
So it's probably not an issue with the net_hierarchy script. But I'm not sure how to proceed. Any suggestions?
Thanks!
Chinedu
________________________________________
From: Matthew Webster [[log in to unmask]]
Sent: Monday, April 18, 2016 10:49 AM
To: [log in to unmask]
Subject: Re: [FSL] Question about nets_hierarchy script
Hello,
Are you able to run linkage using the matlab example data:
load fisheriris
Z = linkage(meas,'ward','euclidean');
Kind Regards
Matthew
On 18 Apr 2016, at 15:29, Anyaeji, Chinedu (NIH/CC/OCRTME) [F] wrote:
> Hi!
>
> This is the error that reads from Matlab (I follow the instructions on the tutorial carefully).
>
> >> nets_hierarchy(Znet1,Znet2,ts.DD,group_maps);
>
> ans =
>
> 99th% abs value below diagonal is 15.734152
>
>
> ans =
>
> 99th% abs value above diagonal is 12.942903
>
> Error: File: linkage.m Line: 1 Column: 1
> The input character is not valid in MATLAB statements or expressions.
>
> Error in nets_hierarchy (line 53)
> yyRSN=linkage(y,'ward');
>
> I've pasted the corresponding portion of the script with the problem below:
>
> --
> figure('position',[10 10 1000 500]); clear y; N=size(netmatL,1); gap=.5/(N+1);
> grot=prctile(abs(usenet(:)),99); usenet=max(min(usenet/grot,1),-1)/2;
> for J = 1:N, for I = 1:J-1, y((I-1)*(N-I/2)+J-I) = 0.5 - usenet(I,J); end; end;
> yyRSN=linkage(y,'ward');
> subplot('position',[0 H2 1 1-H2]);
> if exist('octave_config_info')~=0
> ---
>
> I'm not sure what's wrong. I'm not very familiar with the linkage function but it seems as though the y variable is inappropriately defined. Suggestions?
>
> Thanks!
> Chinedu
>
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>
> Chinedu I. Anyaeji
> Medical Student Research Scholar
> Laboratory of Brain and Cognition,
> NIMH/NIH/DHHS
> 10 Center Drive, 4C212
> Bethesda, MD 20817
> [log in to unmask]
> 301-827-9306
> From: Anyaeji, Chinedu (NIH/CC/OCRTME) [F]
> Sent: Sunday, April 17, 2016 5:26 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Question about nets_hierarchy script
>
> Thank you for the response. Are these the additional toolboxes you were alluding to?
> • Statistics
> • Bioinformatics
> • Signal Processing
>
> Thanks!
> Chinedu
> From: Stephen Smith [[log in to unmask]]
> Sent: Friday, April 15, 2016 11:33 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Question about nets_hierarchy script
>
> Hi
>
> We regularly run this (nets_hierarchy) on matlab and octave without a problem. Have you adapted the script maybe? Is it a reasonably recent version of matlab, and do you have the necessary additional toolboxes installed? We would need to see more details about what you're trying to run and what the error messages are.
>
> Cheers, Steve.
>
>
>> On 15 Apr 2016, at 20:26, Anyaeji, Chinedu (NIH/CC/OCRTME) [F] <[log in to unmask]> wrote:
>>
>> Dear coordinator,
>>
>> Thank you for the FSL tutorials. They are amazing!
>>
>> However, I have a question about one of the FSLNETS scripts. I'm having issues with the nets_hierarchy script and I was wondering if I was missing something. Are there any more recent updates ? I only ask because I repeatedly run into problems when I run it on either Matlab or Octave. On Matlab it says, "the input character (the input for the linkage function) is not a valid matlab expression or statement." On Octave it reads a different error, it seems to be having problems with the dendrogram function... I was wondering if anyone has had this problem or if there is something else I could be potentially doing wrong.
>>
>> Thank you!
>>
>> Chinedu I. Anyaeji
>> Medical Student Research Scholar
>> Laboratory of Brain and Cognition,
>> NIMH/NIH/DHHS
>> 10 Center Drive, 4C212
>> Bethesda, MD 20817
>> [log in to unmask]
>> 301-827-9306
>
>
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> Stephen M. Smith, Professor of Biomedical Engineering
> Head of Analysis, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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