Hi,
On 23 Oct 2006, at 18:12, Paul Geha wrote:
> Hi Steve ,
>
> two more questions:
>
> 1. please correct me if I am wrong: if my t1_stdmask_pve1.nii.gz
> looks fine but the t1_stdmask_pve_1_segperiph has some cortical
> omissions ( seen also in t1_periph_render) this means that the
> segmentation is correct and cannot be improved further ( with
> Fast), but there is a masking problem when we pass from grey to
> peripheral grey to get the cortical volume only?
Exactly.
>
> 2. the output of Sienax called t1_stdmask_segvent and
> t1_stdmask_segperiph come out as completely empty. Does this
> indicate any error of some kind?
Are you sure - it may just be a display range issue in FSLView?
Cheers.
>
> thanks a lot for all the help,
>
> Paul
>
>
>
>
>
>
> At 01:01 AM 10/23/2006, you wrote:
>> You can certainly tune the FAST options - if you put these after -S
>> at the end of the sienax command then when SIENAX calls FAST these
>> get passed on.
>>
>> To get the FAST options type
>> fast -h
>>
>> Cheers, Steve.
>>
>>
>> On 22 Oct 2006, at 22:24, Paul Geha wrote:
>>
>>> thank you Steve,
>>>
>>> so yes the question is : can I use FAST to improve the output of
>>> Sienax?
>>>
>>> Paul
>>>
>>>
>>> ==============Original message text===============
>>> On Sun, 22 Oct 2006 1:32:24 am CST Steve Smith wrote:
>>>
>>> Hi - I'm not sure if you're saying that you'd like to improve the
>>> segmentation output by FAST or the effect of the cortical masking
>>> carried out by affine-transforming a simple cortical standard space
>>> mask onto the data - it sounds like it may be the latter, in which
>>> case you might want to use your own version of $FSLDIR/etc/standard/
>>> avg152T1_strucseg_periph - or it may simply be that your subject is
>>> too different from the MNI152 for a purely affine transformation to
>>> give you a good match of the mask, in which case SIENAX can't help
>>> you there!
>>>
>>> Hope this helps - cheers, Steve.
>>>
>>>
>>> On 21 Oct 2006, at 17:57, Paul Geha wrote:
>>>
>>>> Hello,
>>>>
>>>> I am trying to do a cortical volume quantification using Sienax on
>>>> t1 images. When I run it I get
>>>> the output called t1_periph_render. This one shows that there are
>>>> some small areas in the
>>>> fusiform gyrus, and the orbito-frontal cortex. I tried to
>>>> increase the number of iteration with
>>>> the S option (to 15) in Sienax to improve this but this did not
>>>> work. However, if I run FAST on
>>>> the t1 image with the "use a priori probability maps for
>>>> initialising" I get a better peripheral
>>>> gray matter mask in t1_brain_seg1 image with no omissions, but
>>>> this one includes the sub-cortical
>>>> structures and the cerebellum, which I want to exclude.
>>>>
>>>> Can I improve Sienax segmentation in anyway? Please advise.
>>>>
>>>> thanks a lot,
>>>>
>>>> Paul
>>>>
>>>> Paul Geha M.D.
>>>> Northwestern University
>>>> The Feinberg School of Medicine
>>>> Department of Physiology M211
>>>> 303 E. Chicago Ave.
>>>> Chicago, IL 60611
>>>> Tel:312-503 2886
>>>> Fax: 312-503-5101
>>>
>>>
>>> --------------------------------------------------------------------
>>> -- --
>>> ---
>>> 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--------------------------------------------------------------
>>> -- --------
>>> ---
>>>
>>> ===========End of original message text===========
>>>
>>>
>>>
>>> Paul Geha M.D.
>>> Northwestern University
>>> The Feinberg School of Medicine
>>> Department of Physiology M211
>>> 303 E. Chicago Ave.
>>> Chicago, IL 60611
>>> Tel:312-503 2886
>>> Fax: 312-503-5101
>>
>>
>> ---------------------------------------------------------------------
>> --- ---
>> 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
>> ---------------------------------------------------------------------
>> --- ---
>
> Paul Geha M.D.
> Northwestern University
> The Feinberg School of Medicine
> Department of Physiology M211
> 303 E. Chicago Ave.
> Chicago, IL 60611
> Tel:312-503 2886
> Fax: 312-503-5101
------------------------------------------------------------------------
---
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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