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