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
