Hi,

> fslmaths tbss_tfce_corrp_tstat1.nii.gz -roi -37 4 -42 3 14 11 -o  
> ROI_SLF

This syntax is wrong.  For fslmaths the -roi command is:
  -roi <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> :  
zero outside roi (using voxel coordinates)

That is, it must be followed by 8 numbers (not 6 like yours) and
they must be in voxel coordinates and thus positive (unlike yours).
Also, there is no -o command.  You just put the required output
name at the end of the command, much like the fslmaths call
that you do below.

> fslmaths ROI_SLF -mas mean_FA_skeleton_mask myfinal_mask
>
> fslmeants -i all_FA_skeletonised -m ROI_SLF -o output_filename.txt

The rest here looks fine.

All the best,
	Mark


>
> I surfed a bit in FSL archives and found some messages also with the  
> same issue... but could find and answer...
>
> what am  I doing wrong?
>
> thanks again!
>
>
>
> On Wed, Sep 1, 2010 at 8:22 AM, Stephen Smith <[log in to unmask]>  
> wrote:
> Hi,
>
> On 31 Aug 2010, at 22:11, Francisca Serrano wrote:
>
>> Hi
>> I have still questions in FA values extraction....I've used the  
>> commands
>>
>> fslmaths tbss_tfce_p_tstat1.nii.gz -thr 0.95 -bin  
>> tbss_tfce_p_tstat1_mask
>>
>> fslmeants -i all_FA_skeletonised -m tbss_tfce_p_tstat1_mask -o  
>> tbss_tfce_p_tstat1.txt
>
> This is fine as long as you meant to use the *uncorrected* p-values  
> for this mask, as opposed to the *corrected* p-values.
>
>> to extract FA values after the TBSS whole procedure... Now I wonder  
>> if these values correspond to the mean significant FA values in all  
>> brain tracts (all the skeleton), and how to extract FA values from  
>> only one part of the tracts that I see in red... For example, let's  
>> say that I see significant FA in both right and left parts of  
>> superior longitudinal fasciculus, but I only want to have FA values  
>> of the left part.
>>
>> I thought to used fslroi to select only that one part, using
>>
>> fslroi tbss_tfce_p_tstat1.nii.gz roi 126 5 79 6 88 15   - following  
>> the command fslroi <input> <output> <xmin> <xsize> <ymin> <ysize>  
>> <zmin> <zsize>
>
> This is wrong because fslroi reduces the size of the image - so it  
> will no longer match the all_FA_skeletonised image.
> You're close though - you should use the -roi option in fslmaths
>
> Cheers.
>
>
>
>>
>> and then
>>
>> fslmeants -i all_FA  -m roi.nii.gz -o roiFA_allsubjects.txt
>>
>> to have the FA values in that exact part...
>>
>> but the last command is not giving me any result....
>>
>> am I mixing things? is fslroi what i have to use or maybe cluster  
>> command?
>>
>> thanks in advance for the help!
>>
>> Francisca
>>
>>
>>
>> On Tue, Aug 17, 2010 at 4:33 PM, Gwenaëlle DOUAUD <[log in to unmask] 
>> > wrote:
>> Hi Francesca,
>>
>> fsmeants -i all_FA_skeletonised  -m mean_FA_skeleton -o  
>> FA_forallmysubjects.txt
>> or
>> fsmeants -i all_FA_skeletonised  -m significant_results_mask -o  
>> significant_FA_forallmysubjects.txt (where you would get the mask  
>> of your significant results by doing something like: fslmaths  
>> results_***_corrp.nii.gz -thr 0.95 -bin significant_results_mask)
>>
>> For the 2x2, if you have two groups and two time-points, have a  
>> look at my recent post in the FSL archives: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1008&L=FSL&P=R8137&1=FSL&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4
>>
>> Cheers,
>> Gwenaëlle
>>
>>
>> De: Francisca Serrano <[log in to unmask]>
>> Objet: [FSL] extract numerical FA values after TBSS in FSL
>> À: [log in to unmask]
>> Date: Mardi 17 août 2010, 19h45
>>
>> Hi,
>>
>> I have been working with FSL and TBSS tool, and after arriving to  
>> the step 4 (tbss_4_prestats) and be able to see the images  
>> resulting from Randomise and voxelwise statistics on the  
>> skeletonised FA data I wonder how can I get numerical values of the  
>> differences that it could be inferenced from the images to do  
>> correlations with behavioral data.
>>
>> I also wonder about the posibility to do an ANOVA 2x2 using TBSS  
>> statistics.
>>
>> Thanks in advance!
>>
>> Francisca
>> --------------------------------------------------------------------
>>
>> Gwenaëlle Douaud, PhD
>>
>> FMRIB Centre, University of Oxford
>> John Radcliffe Hospital, Headington OX3 9DU Oxford UK
>>
>> Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
>>
>> www.fmrib.ox.ac.uk/~douaud
>>
>> --------------------------------------------------------------------
>>
>>
>
>
> ---------------------------------------------------------------------------
> 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)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
>