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Hello FslNets Experts,

I think I had read fSLwiki on Group ICA, dual regression and FSL Nets.
Now also I am getting error

/bin/bash: slices_summary: command not found
Error using imread (line
350)
File "grot.png" does not
exist.

Error in nets_pics (line 4)
picgood=imread('grot.png');
figure; imagesc(picgood);
axis off; title('good
components');

Error in my_nets (line 33)
nets_pics(ts,group_maps);
% quick views of the good
and bad components

I have installed FSL 5.0 and set the path in matlab by selecting the following folders

/usr/share/fsl/5.0/bin

/usr/share/fsl/5.0/etc/matlab

path/to/FSLNets

I had made the slices_summary script executable by

chmod 755 slices_summary, but now also I find the error

/bin/bash: slices_summary: command not found

Kindly assist us in running network analysis using FSLNets

On Tue, Apr 23, 2013 at 11:43 AM, Himanshu Joshi <[log in to unmask]> wrote:

Hello Stephen,
I suppose dual regression had worked fine,
because the time courses are in output form and modified nets_example.m (i.e. myfslnets.m) also plots all the subject specific time courses before giving the error

pngappend: error while loading shared libraries: libutils.so: cannot open shared object file: No such file or directory

Error using imread (line 369)
File "grot.png" does not exist.

Error in nets_pics (line 4)
picgood=imread('grot.png'); figure; imagesc(picgood); axis off; title('good components');

Error in myfslnets (line 33)
nets_pics(ts,group_maps); % quick views of the good and bad components

Please comment what could be the reason
On Sat, Apr 20, 2013 at 6:50 PM, Stephen Smith <[log in to unmask]> wrote:
Hi - I think you need to start from the beginning making sure everything is working correctly. Carefully read the manuals on the FSL wiki on group-ICA, dual-regression and FSLNets. If the dual-regression has worked correctly, the subject timecourses should be in the output from that (check that they are), and FSLNets (if setup correctly) can be pointed at that directory and load in those time series fine with nets_load.

Steve.
On 20 Apr 2013, at 07:16, Himanshu Joshi <[log in to unmask]> wrote:
I had fixed the paths now I am having problem like
Error using -
Matrix dimensions must agree.

Error in nets_load (line 32)
grot=grot-repmat(mean(grot),size(grot,1),1); % demean

Error in demfslnets (line 24)
ts=nets_load(ts_dir,3,1);

please comment
On Fri, Apr 19, 2013 at 10:05 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,
Do you still have errors like this:
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/imtest: not found
If so then you still have to fix your paths.

All the best,

Mark
On 19 Apr 2013, at 13:42, Himanshu Joshi <[log in to unmask]> wrote:
sorry,
the line i mean to say was

Does slices_summary program creates this if so I dint find after the execution of the script using matlab?

sorry for the inconvinence
On Fri, Apr 19, 2013 at 6:05 PM, Himanshu Joshi <[log in to unmask]> wrote:
Thanks Mark,

I had set the path but still I am having a problem

I wonder there is no such file like melodic_IC.sum/0000.png in /home/mv/Desktop/Test/all.gica/groupmelodic.ica

How it can be opened

does slices_summary programm creates this if so I dint find that in the script.

Cannot open /home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC.sum/0000.png for reading
Segmentation fault (core dumped)
slices_summary /home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC.sum grot.png 0 1 2 3 4 5 6 8 10 13 14 16 17: Segmentation fault
Error using imread (line 369)
File "grot.png" does not exist.

Error in nets_pics (line 4)
picgood=imread('grot.png'); figure; imagesc(picgood); axis off; title('good components');

Error in myfslnets (line 33)

nets_pics(ts,group_maps); % quick views of the good and bad components

please suggest what could be the problem

Thanks and regards
On Wed, Apr 17, 2013 at 3:48 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

The path you add to matlab should be /usr/share/fsl/5.0/etc/matlab and not /usr/share/fsl/etc/matlab

All the best,
    Mark




Himanshu Joshi <[log in to unmask]> wrote:
I had upgraded fsl to fsl 5.0

but again the error is
Warning: Name is nonexistent or not a directory: /usr/share/fsl/etc/matlab.
> In path at 110
In addpath at 87
In myfslnets at 13
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/imtest: not found
/usr/share/fsl/5.0/bin/slices_summary: 97: [: =: unexpected operator
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found
/usr/share/fsl/5.0/bin/slices_summary: 1: /usr/share/fsl/5.0/bin/slices_summary: /usr/share/fsl/bin/zeropad: not found

Cannot open /home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC.sum/.png for reading
Segmentation fault (core dumped)
slices_summary /home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC.sum grot.png 0   1   2   3   4   5   6   8 10 13 14 16 17: Segmentation fault
Error using imread (line 369)
File "grot.png" does not exist.

Error in nets_pics (line 4)
picgood=imread('grot.png'); figure; imagesc(picgood); axis off; title('good components');

Error in myfslnets (line 33)
nets_pics(ts,group_maps);                % quick views of the good and bad components

PLEASE suggest How should I tackle the issue

On Tue, Apr 16, 2013 at 5:17 PM, Himanshu Joshi <[log in to unmask]> wrote:

I will consider your sugesstion and upgrade my fsl to 5.0

but for the time being I had downloaded the slices_summary script and made it executable

now error 1 regarding slices_summary is not there now the problem is

Cannot open /home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC.sum/0000.png for reading
Segmentation fault (core dumped)
slices_summary /home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC.sum grot.png 0   1   2   3   4   5   6   8 10 13 14 16 17: Segmentation fault

Error using imread (line 369)
File "grot.png" does not exist.

Error in nets_pics (line 4)
picgood=imread('grot.png'); figure; imagesc(picgood); axis off; title('good components');

Error in myfslnets (line 33)
nets_pics(ts,group_maps);

I am providing group_maps as
group_maps='/home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC

yes there is no such file exists like melodic_IC.sum/ 0000.png

I dont know I suppose myfslnets.m will create this

any comments

On Tue, Apr 16, 2013 at 11:12 AM, Watson, Christopher <[log in to unmask]> wrote:

Hi Himanshu,
I think the #1 suggestion will be to upgrade to the latest version of FSL, and then see if you have any problems.

________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Himanshu Joshi [[log in to unmask]]

Sent: Tuesday, April 16, 2013 1:40 AM

To: [log in to unmask]
Subject: Re: [FSL] What should a ts_dir directory of nets_example.m script making use of FSLNets contain?

I have FSL 4.1 installed
and $FSLDIR is set as
FSL_DIR /usr/share/fsl/4.1

shall I set it as /usr/share/fsl/4.1/bin

On Mon, Apr 15, 2013 at 4:39 PM, Stephen Smith <[log in to unmask]<mailto:[log in to unmask]>> wrote:
This means you either don't have the most recent FSL or $FSLDIR/bin isn't in your path.

On 15 Apr 2013, at 10:45, Himanshu Joshi <[log in to unmask]<mailto:[log in to unmask]>> wrote:

After using the suggested script, the time-series plot for all components is plotted mentioning the error

/bin/bash: slices_summary: command not found
Error using imread (line 369)
File "grot.png" does not exist.

Error in nets_pics (line 4)
picgood=imread('grot.png'); figure; imagesc(picgood); axis off; title('good components');

Error in myfslnets (line 33)
nets_pics(ts,group_maps); % quick views of the good and bad components

On Mon, Apr 15, 2013 at 12:51 PM, Stephen Smith <[log in to unmask]<mailto:[log in to unmask]>> wrote:

On 15 Apr 2013, at 08:17, Himanshu Joshi <[log in to unmask]<mailto:[log in to unmask]>> wrote:

Hello lovely people,

I am using FSLNets for finding correlations among the spatial maps using nets_examples.m. I had copied it to another file named myfslnets.m, but while using the script I have a confusion that What should we provide at ts_dir=GroupICA.dr ?

I am unable to find .dr file in my dual regression output directory.

I had a dual regression output directory containing all subjects time-series named
dr_stage1_subject00000.txt...dr_stage1_subject0001.txt..........till 20 subjects

I suppose I have to provide the address of this dualregression output folder like
ts_dir= '/home/mv/Desktop/Test/dualreg_output';

yes

I am not sure about this sign- ' is required or not in the script

Thanking you in anticipation

--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Ph.D Scholar
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html

---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717) 2176

[log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve

---------------------------------------------------------------------------

--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html

---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717) 2176

[log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve

---------------------------------------------------------------------------

--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html

--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html

--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717) 2176
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html

Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Ph.D Scholar,
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html