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Subject:

Re: fMRI analysis and FEAT

From:

Christian Beckmann <[log in to unmask]>

Reply-To:

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

Date:

Thu, 10 Jan 2002 23:21:58 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (114 lines)

Hi Eric

Eric J Feczko wrote:

> Hi Steve, this is Eric Feczko. I have just started using FSL and I have a couple
> of questions concerning the results that FEAT produces and a question about the
> setting up the design matrix. In our study, a subject is presented with a series
> of faces for which there are seven conditions: happy, sad, fearful, neutral,
> angry, suprise, and disgust. We run the experiment four times on the subject,
> and each run's timing for the presentation is different. Since FSL can only
> analyze more than one subject when the timing is the same for all runs,


Not quite, if you want to analyze multiple subjects, then the individual
design matrices for each *subject* need to be the same.

should I
> cocatenate all the runs together and then analyze each subject, or can I just
> analyze each run separately, and then do a group analysis combining all four
> runs for each subject?


You can concatenate the individual runs for each subject provided the
data was taken in one go - otherwise there is the chance of the runs
having different base level intensities etc. which would interfere with
the filtering etc. In that case you're better off analysing each run
seperately.


>I also have two questions about the results. First, how
> can I acquire all the data from each voxel cluster?


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


> And second, I noticed that
> all the .GIF files were sliced from a coronal view. Is there a way to reslice
> the images produced by FEAT from different orientations?


The final maps are stored as AVW files called 'Rendered_thresh_zstat*'
and can be found in the .feat folder. Feat uses a program called
'slicer' to generate the gif files that appear in the report.html. What
is being produced will depend on the orientation of the brain within
your 4D avw files. The .gif inside the feat report is produced along the
z direction of the data file - if you want to view the results in a
different direction you can either specify individual slices to be
generated by slicer, e.g.

slicer infile -x -20 outfile.gif  will produce a gif of the 20th slice
in x direction etc.

or you can re-orient the Rendered_thresh_zstat images using the flirt
registration program. If you want to re-orient the original data, you
can use 'applyxfm4D'. For a descibtion on how to generate the flirt
matrix have a look at the FSL archive

http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0111&L=fsl&D=0&P=5536

hope this all makes sense

Christian














If you can provide any
> help in this matter that would be great, thanks!
> -Eric
>
>
>


--
  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

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