Dear Steve and Ged,
this is the solution that settled on for making masks for the
hippocampus for my subjects. i am wondering if you can tell me what you
think of it. also, i have run into a new problem. i will greatly
appreciate any advice on how to solve it.
here is what i did:
i ran the structural runs of a subject through Freesurfer to get the
automated probabilistic cortical and subcortical segmentation maps for
this subject.
Then i followed the steps under "CORTICAL AND SUB-CORTICAL
SEGMENTATIONS" (http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html) to
generate binary masks for this subject's hippocampus to use in FSL.
running
avwmaths featdir/reg/freesurfer/aseg.nii.gz \
-thr 17 -uthr 17 \
featdir/reg/freesurfer/lh.hippocampus.nii.gz
will give me a mask in the space of my functional runs. this mask is
either 0 or 17 (0 being background and 17 being hippocampus). all is
good so far.
next, i tried to re-sample this mask to the highres space using flirt
and example_func2highres.mat. the re-sampled mask has two problems: 1)
it becomes too wide in x, y and z and 2) it has continuous values from 0
to 17. i cannot just threshold the new mask at 17, because i will miss
major parts of the hippocampus, and i cannot use it because it is too
wide. any suggestions on how i can solve these two problems?
thanks
paymon
Ged Ridgway wrote:
> Hi Paymon,
>
> As Steve implies, I don't think maps yet exist for avg152, however, you
> can get some probabilistic maps for ICBM452, which may include some
> structures of interest to you...
>
> http://www.loni.ucla.edu/ICBM/ICBM_Probabilistic.html
>
> Also, I believe people have got approximate masks for e.g. the ICBM
> single subject template (AKA Colin27), though these aren't the same as
> probabilistic population templates, they may be all you need for a basic
> and rough ROI analysis. See e.g. Tzourio-Mazoyer et al's AAL stuff for
> SPM (should be pretty easily converted to separate NIfTI ROIs)
>
> http://www.cyceron.fr/freeware/
>
> Hope that helps,
> Ged.
>
> Steve Smith wrote:
>> Hi - we will be generating such probabilistic maps in the near future,
>> watch this space.
>> Cheers.
>>
>> On 22 Nov 2006, at 22:25, Paymon Hosseini wrote:
>>
>>> Dear FSL users,
>>>
>>> i am wondering if there are structural masks for the standard brain
>>> (avg152T1_brain) in FSL. For example, is there a mask for the
>>> hippocampus or the amygdala?
>>>
>>> thanks a lot,
>>> paymon
>>
>>
>> ---------------------------------------------------------------------------
>>
>> 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
>> ---------------------------------------------------------------------------
>>
>>
