Hi Steve,
Thank you for your response. When I do getenv('FSLOUTPUTTYPE') in matlab, it throws
ans =
''
So I included setenv('FSLOUTPUTTYPE','NIFTI_GZ') in the startup.m file, and it works. However, I have another error message. At the line 64 of my_nets.m where randomise run, it seems run correctly but after that gives the following error message:
###################################
.
.
.
Starting permutation 4998
Starting permutation 4999
Starting permutation 5000
Critical Value for: /private/tmp/tp86c08685_d05e_4eb5_9093_9db7e4ab7709_vox_corrp_tstat2 is: 3.18253
Finished, exiting.
Error using fileparts
Too many output arguments.
Error in read_avw (line 18)
[PATHSTR,NAME1,EXT,VERSN] = fileparts(fname);
Error in nets_glm (line 28)
p_uncorrected(i,:)= read_avw(sprintf('%s_vox_p_tstat%d',fname,i));
Error in my_nets (line 64)
[p_uncorrected,p_corrected]=nets_glm(netmat1,'design.mat','design.con',1); % returns matrices
of 1-p
####################################
Could you give me any advice? This time I'm completely at a loss.
"This must mean that you don’t have FSL correctly setup in the shell that is calling matlab."
Does this mean I need to start matlab from the same terminal as FSL? I'm a Mac User (OS 10.6) and starting FSL from Mac Terminal, while starting Matlab from the icon in the Dock.
Thank you very much,
Jun Miyata
Hi
On 15 Nov 2013, at 15:13, Jun Miyata <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I'm trying FSLNets and recently had the following errors when running nets_examples.m (renamed as my_nets.m):
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=fsl&P=R49242&1=fsl&9=A&I=-3&J=on&K=1&d=No+Match%3BMatch%3BMatches&z=4
>
> I have solved this problem with the following:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=fsl&P=R49499&1=fsl&9=A&I=-3&J=on&K=1&d=No+Match%3BMatch%3BMatches&z=4
>
> But now I have another problem. At the line 59 of my_nets.m, I get the following warning:
>
>
> Warning: ward's linkage specified with non-Euclidean dissimilarity matrix.
>> In linkage at 171
> In nets_hierarchy at 26
> In my_nets at 59
yes - I get this warning too - ignore it.
>
>
> But the script goes on, and when it come to the line 64, I get the following error:
>
>
> randomise options: -i /private/tmp/tp91169492_0789_46ac_8144_fe8a16b61b2e -o /private/tmp/tp91169492_0789_46ac_8144_fe8a16b61b2e -d design.mat -t design.con -x -n 5000
> ERROR:: Environment variable FSLOUTPUTTYPE is not set!
This must mean that you don’t have FSL correctly setup in the shell that is calling matlab.
Cheers.
> Please make sure that the appropriate configuration file is sourced by your shell (e.g. by putting it in .profile).
> e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh"
> e.g. tcsh or csh users add the line "source ${FSLDIR}/etc/fslconf/fsl.csh"
> Loading Data: Error in nets_glm (line 3)
> XXX=size(netmat,2);
>
> Output argument "p_uncorrected" (and maybe others) not assigned during call to
> "/Users/JMmacpro/matlab/FSLNets/nets_glm.m>nets_glm".
>
> Error in my_nets (line 64)
> [p_uncorrected,p_corrected]=nets_glm(netmat1,'design.mat','design.con',1); % returns matrices
> of 1-p
>
>
> Of course FSLOUTPUTTYPE is set. If I do "echo $FSLOUTPUTTYPE" in the terminal outside matlab it returns "NIFTI_GZ". Also the line ". ${FSLDIR}/etc/fslconf/fsl.sh" is included in my .bash_profile.
>
> I found a similar error report in the mailing list:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1306&L=fsl&P=R126049&1=fsl&9=A&I=-3&J=on&K=1&d=No+Match%3BMatch%3BMatches&z=4
>
> According to this, the warning sign itself seems normal. But in my case the problem is not the design files but FSL output file type.
>
> How can I solve the problem? Is this related to my solution to the first problem? Any help is appreciated.
>
> Jun Miyata
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