FIVE documentation

[Meg Spriggs]

Hello,

I was wondering if there any way to get some documentation on using FIVE. I have just analysed my data using GLMFlex2 and I am wanting to view it. I have downloaded FIVE, but I am a little confused about using it. Is it the best way to veiw data from GLMFlex?

Thanks
Meg

[Aaron Schultz]

You can view the results in any image viewer that you like (e.g.
xjview, mricron, fslview, etc...). I obviously prefer FIVE, but then
I wrote it, so that's not a big surprise. I don't have any
documentation put together for FIVE, so you will just need to do some
exploring, but if you have specific questions, please post them to the
list.

The special advantage for using FIVE is extracting data from and
plotting results for voxels blobs or spheres, which only works with
GLM Flex/Flex Fast models, though it has many other bells and whistles
for looking at data, and making figures.

To run FIVE, just type FIVE;

This will bring up the FIVE viewer with a default MNI152 underlay.

Next click the "Open Image" button, and select the map you want to open.

Use the threshold and limit boxes to set and adjust the color maps.

If you want to plot something right click the image and you will see
plotting options for the current coordinate.

-Aaron

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[Meg Spriggs]

Cool thanks for your reply, 

This might be a really silly question but is there any way to get results tables, like the ones you get in SPM, through FIVE? 

Thanks for all your help. 

Meg

[MCLAREN, Donald]

Yes. You need to click find peaks after downloading the peak_nii toolbox (I forget if its included in the download or not). I can be found at: http://martinos.org/~mclaren/ftp/Utilities_DGM/ and will soon be moved to nitrc (www.nitrc.org/projects/peak_nii)

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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[Meg Spriggs]

Thank you I will do that. 

Meg

On Wednesday, April 9, 2014 3:30:33 PM UTC+12, Meg Spriggs wrote:

[Meg Spriggs]

Hello again,

I am just having some trouble with FIVE, I tried to plot the cluster and I got this error message:

Reading in original input files
Undefined function 'GLM_Plot' for input arguments of type 'struct'.

Error in FIVE/plotVOI (line 3153)
                 [yres xres] = GLM_Plot(VOI,777+gcf);
 
Error while evaluating uimenu Callback


Also, I have downloaded the peak_nii toolbox but there is no option saying 'find peaks', and when I click 'get peak info' i get this error message:

Error: File: peak_nii_inputs.m Line: 300 Column: 82
Unexpected MATLAB operator.

Error in peak_nii (line 96)
[invar, errors, errorval]=peak_nii_inputs(mapparameters,infoI1.fname,nargout);

Error in FIVE/getPeakInfo (line 3331)
        [peak.voxels peak.voxelstats peak.clusterstats peak.sigthresh peak.regions] =
        peak_nii(Obj(vn).FullPath(1:end-2),S);
 
Error while evaluating uimenu Callback


I might be doing something really silly, I am not very good at using MatLab, but any suggestions would help.

Thanks for your time,

Meg


On Wednesday, April 9, 2014 3:30:33 PM UTC+12, Meg Spriggs wrote:

[MCLAREN, Donald]

I'll send out a bug fix tonight.

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[Meg Spriggs]

Thank you =)

On Wednesday, April 9, 2014 3:30:33 PM UTC+12, Meg Spriggs wrote:

[Aaron Schultz]

The GLM_Plot error is being caused because matlab cannot find the
GLM_Plot function. Make sure that you it's in the Utilities folder,
and make sure that folder has been added to the matlab path.

-Aaron

[Meg Spriggs]

my file for FIVE and the Utilities file are both in the MatLab path. But if I look in the folders there is no GLM_Plot script, but there is a GLM_Plot2. Is that what it suppose to be using?

Meg



On Wednesday, April 9, 2014 3:30:33 PM UTC+12, Meg Spriggs wrote:

[MCLAREN, Donald]

Here are updated peak_nii files.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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[Aaron Schultz]

There should be a GLM_Plot script.  Add the attached file to the scripts and see if that fixes the problem.

-Aaron

[Meg Spriggs]

Thank you :)

[Meg Spriggs]

Hello,

Im sorry to bother you again, but I have tried running peak_nii, and I am getting this error:

Using default option of whole brain for statistics, even if there is a mask.
Using the default of no RESELS. FWHM was incorrectly specified or missing.
Using the default corrected threshold of p<0.05.
Threshold is:3.7328
Undefined function 'peak_get_lm18' for input arguments of type 'double'.

Error in peak_nii (line 373)
                INDEX18 = peak_get_lm18(Iuse,L');

Error in FIVE/getPeakInfo (line 3331)
        [peak.voxels peak.voxelstats peak.clusterstats peak.sigthresh peak.regions] =
        peak_nii(Obj(vn).FullPath(1:end-2),S);
 
Error while evaluating uimenu Callback

Am I doing something really silly?
I really appreciate all the help you have giving me =)

Thanks a lot!!!!!!

Meg


On Wednesday, April 9, 2014 3:30:33 PM UTC+12, Meg Spriggs wrote:

[MCLAREN, Donald]

You need to compile the mex files:

Go into the peak_nii directory, then in MATLAB, run the following commands:

mex peak_get_lm18.c

mex peak_get_lm6.c

mex peak_get_lm26.c

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
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[Meg Spriggs]

I am now getting this error message. Does this mean I am using the wrong verison of matlab?



 mex peak_get_lm18.c

Warning: You are using gcc version "4.6.3-1ubuntu5)".  The version
         currently supported with MEX is "4.4.6".
         For a list of currently supported compilers see:
         http://www.mathworks.com/support/compilers/current_release/

/usr/bin/ld: cannot find -lstdc++
collect2: ld returned 1 exit status

    mex: link of ' "peak_get_lm18.mexa64"' failed.

Error using mex (line 206)
Unable to complete successfully.

[MCLAREN, Donald]

I would contact your system administrator to get the correct compiler. It looks like you might be able to download one from the MATLAB link provided.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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[yayua...@gmail.com]

DEAR experts,

I amnew to FIVE and after I set path and saved, I entered "FIVE" in the command window, there is an error coming out as

 Index exceeds matrix dimensions.

Error in openIMG (line 28)

[a b c] = fileparts(strtrim(fn(1,:)));

Error in FIVE (line 108)

    [I h] = openIMG(which('defaultUnderlay.nii'));

I don't know where goes wrong.

Hope you can point out.

Thanks a lot.

[Aaron Schultz]

Did you also download the utilities and add those to your matlab path?

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[Charlotte Vogt]

Hey guys,

I encounter the same problem (and error message) when trying to open FIVE, even though I downloaded the utilities package and added it to my matlab path. Any ideas?

Thank you so much in advance!

Best, Charlotte

[Aaron Schultz]

What was the nature of the error message?

-Aaron