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
