Hi Eric,

I'm not quite sure what it is you're looking for, if you're interested
in the summary statistics for each cluster, these appear as .html and
raw txt files in the feat report and can be found in the .feat directory
as cluster_z{f}stat*.{html,txt}. If you want the full set of data rather
than the summary stats for each voxel, you can use the cluster mask for
each cluster (generated as described in the previous mail) and use that
to threshold the zstat image, i.e.

avwmaths thresh_zstatX -mas cluster_maskY output


you can use all the other avw tools on output, e.g. if you want to know
the value and location of the maximum voxel for the specific cluster
(which is the value reported in the report.html) this can be done using

avwstats output -R   (min & max value in the file output)
avwstats output -x   (for the X,Y,Z indices of the max voxel)

If you want the entire cluster as a text file

avw2ascii output  filename.txt

That's gonna be a huge file but you can use

avwstats output -w

in order to find the smallest ROI containg all the non-zero voxels
within the avw file output. Then use avwroi to extract a smaller region
of interest that contains the cluster before converting to text format.

Also, there is avwmeants that, given any file will and possibly a mask,
will produce the mean of all the time courses. With the -v option on,
you can pipe all values in you file into an additional text file.

Generally, the avwutils (all in $FSLDIR/bin) are used quite heavily used
in FSL and an almost complete desciption of what's there is at

http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html


hope this helps

Christian





















Eric J Feczko wrote:

> Thanks for the help! I was able to re-orient the data using FLIRT, and decided
> to analyze each run separately, but I am still having trouble finding the stats
> from each cluster. I know you showed me how to acquire a specfic cluster and
> make a mask for the data using that, but I was wondering where one can find the
> information on each voxel in numbers(i.e. a file containing the Zmax, etc. and
> co-ordinates of each voxel). I apologize for the misunderstanding, and if you
> could help me with this that would be great, thanks!
> -Eric
>
>
>
> Quoting Christian Beckmann <[log in to unmask]>:
>
>
>>There is a file called cluster_mask_zstat* in the .feat directory that
>>labels each voxel according to the cluster it belongs to, e.g. if
>>there
>>are 10 clusters in the zstat image, this file contains integer values
>>from 0 to 10. You can easily check for the number of clusters using
>>'avwstats cluster_mask_zstatX -R'.  This can be used to generate masks
>>using 'avwmath' (both programs come with fsl)
>>
>>If you're interested in generating a 4D AVW file that only contains
>>those voxels that are within cluster Y of the zstat image X, say, you
>>would need to
>>
>>i) generate a mask from the cluster_mask_zstatX file :
>>   'avwmaths cluster_mask_zstatX -mult -1 -thr -Y -mult -1 -thr Y
>>mask_filename'
>>
>>ii) use this mask to threshold the 4D data :
>>   'avwmaths filtered_func_data -mas mask_filename newdata_filename'
>>
>>
>>newdata_filename then is a 4D AVW file of the same size as the
>>original
>>data where only voxels contained within cluster Y of zstatX have
>>non-zero time course
>>
>>
>>  Christian F. Beckmann
>>  Address: Oxford University Centre for Functional
>>           Magnetic Resonance Imaging of the Brain,
>>           John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>  Email:   [log in to unmask]
>>http://www.fmrib.ox.ac.uk/~beckmann/
>>  Phone:   +44(0)1865 222713 Fax: +44(0)1865 222717 Mob: +44(0)7980
>>691852
>>
>>
>
>


--
  Christian F. Beckmann
  Address: Oxford University Centre for Functional
           Magnetic Resonance Imaging of the Brain,
           John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
  Email:   [log in to unmask]  http://www.fmrib.ox.ac.uk/~beckmann/
  Phone:   +44(0)1865 222713 Fax: +44(0)1865 222717 Mob: +44(0)7980 691852