Thanks a lot
I just want to check does FAST put the segmentations into standard space?
if so why can't I open the outputs in fslview and add standard?
do I need to go back into FAST and add the advanced options
* Use apriori prob maps for intialisation? and add for final segmentation?
Thanks in advance
Ciara
>>> Stephen Smith 09/04/10 9:43 >>>
Hi
On 8 Apr 2010, at 18:24, Ciara McCabe wrote:
> Dear FSLers
>
> I need to get WM and CSF covariates to add as nuisance variables in
> my analysis
> Ive begun to use FAST to segment my struct T1 images
>
> i get out image_seg_0.nii.gz, image_seg_1.nii.gz, image_seg_2.nii.gz
>
> how do I know which are the WM and CSF images
look at them!
> and how do i then threshold them so that they are 80% tissue type
> probability?
I would use conservative masks, thresholding high and then eroding,
for example:
fslmaths image_seg_whatever -thr 0.8 -bin -ero maskoutput
and then check visually that this mask makes sense.
> do i then run this mask on the data and get the time series and add
> as another confound ev?
yes - you can use fslmeants
Cheers.
>
> any help much appreciated
>
> Ciara
>
>
>
>
> Dr Ciara McCabe
> Neurosciences Building
> Department of Psychiatry
> Warneford Hospital
> University of Oxford
> Warneford Lane
> Oxford
>
> Tel:01865 223778
> mob:07966035631
> E:[log in to unmask]
> http://www.psychiatry.ox.ac.uk/research/researchunits/perl/perlmembers/ciaramccabe/
>
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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
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