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FSL  December 2012

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Subject:

Re: first_utils and 4D output file

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 13 Dec 2012 09:58:43 +0000

Content-Type:

text/plain

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text/plain (51 lines)

Hi,

It sounds like you are running the older style of vertex analysis, as in FSL 5.0.0 and later we produce nifti images as outputs from vertex analysis, not vtk files.

The vtk outputs in FSL4 have always been tagged by the EV number that they are associated with, as the old style of vertex analysis produced a separate result for each column (EV) in the design matrix.  This is why you get L_Caud_all1.vtk  (the option -o specifies the basename for the outputs, which will be added to with a number and the .vtk extension).

If you want the new version (nifti image outputs suitable for randomise and hence more general statistical tests, involving contrasts) then you will need to make sure you are using FSL5 (the latest version is 5.0.2 which is what we recommend).

All the best,
	Mark


On 7 Dec 2012, at 17:50, Laurence O'Dwyer <[log in to unmask]> wrote:

> Hello FSLers, 
> 	         I have a question regarding the output from "first_utils". 
> We have used "run_first_all" successfully completed on a large dataset. 
> I would like to run a test of the vertex analysis on a sample of 10 controls and 10 disease subjects, and am running: 
> 
> $ first_utils --vertexAnalysis --usebvars -i L_Caud_all.bvars -d two_group.mat -o shape_analysis/L_Caud_all --useReconNative --useRigidAlign -v >& shape_analysis/L_Caud_all.txt
> 
> This processes without an error message and gives the following output: 
> L_Caud_all1.vtk  
> L_Caud_all.txt
> 
> The output should include a 4D image that can be processed via "randomise", and I'm unclear as to why this file is not generated from the above command. 
> I'm also unclear as to why the output is called "L_Caud_all1.vtk" and not "L_Caud_all.vtk" as specified in the with the -o flag the above first_utils command. 
> 
> The mat file used above is: 
> #######################
> /NumWaves	1
> /NumPoints	10
> /PPheights		2.000000e+00
> 
> /Matrix
> 1.000000e+00	
> 1.000000e+00	
> 1.000000e+00	
> 1.000000e+00	
> 1.000000e+00	
> -1.000000e+00	
> -1.000000e+00	
> -1.000000e+00	
> -1.000000e+00	
> -1.000000e+00	
> #############################################
> 
> Any pointers as to possible errors would be appreciated. 
> 
> Cheers; Larry 
> 

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